PANGEA: Personalized Antibodies for Gastro-Esophageal Adenocarcinoma
Phase: PHASE2
Conditions: Adenocarcinoma
Sponsor: University of Chicago

1 
 
Local Protocol #: IRB14-0141 
 
 
 
 
 
 
Version 9 Date 06/19/2018 
 
TITLE:  
 
 PANGEA-IMBBP: Personalized ANtibodies for Gastro-Esophageal Adenocarcinoma -   
 
 
 
 
 
 
A 1st Pilot Metastatic Trial of Biologics Beyond Progression  
 
Trial Design: Expansion Platform Design Type II 
 
Coordinating Center:    University of Chicago Medical Center 
 
*Principal Investigator:    
Daniel Catenacci, MD 
5841 S. Maryland Ave. MC2115 
Chicago, IL 60637 
Phone: 773-702-7596 
Fax: 773 702 9268 
 
 
 
 
 
 
 
Email: dcatenac@medicine.bsd.uchicago.edu 
   
Statisticians:  
 
 
 
 
 
 
 
     Study Coordinator/Data Manger: 
Theodore Karrison, Ph.D.        
 
 
 
 
 
Leah Chase,  
Yuan Ji, Ph.D. 
 
 
 
 
 
 
Clinical Research Associate 
University of Chicago 
 
 
 
 
 
 
University of Chicago 
5841 S. Maryland Ave. MC 2007 
 
 
Section of Hematology/Oncology 
Chicago, IL 60637 
 
 
 
 
 
 
Chicago, IL 60637 
(773) 702-9326 
 
 
 
 
P: 773-834-1472; F: 773-834-1798 
tkarrison@health.bsd.uchicago.edu  
            lmchase@medicine.bsd.uchicago.edu  
 
Responsible Research Nurse: 
 
 
Pathologists and CytoGenetics:  
Sara Covert, RN 
 
 
 
 
John Hart, MD 
University of Chicago Medical Center 
  
 
 
Shu-Yuan Xiao, MD 
5841 S. Maryland Ave., MC 2115     
 
 
      Carrie Fitzpatrick, PhD 
Chicago, IL 60637 
 
 
 
 
 
University of Chicago Medical Center 
 
 
Tel (773)  834-0475 
 
 
 
 
 
Department of Pathology 
Fax (773) 702-3163 
 
 
 
 
 
Chicago, IL 60637 
Sara.Covert@uchospitals.edu 
 
 
P: 773 702 9319 
 
 
 
 
  
 
           John.Hart@uchospitals.edu 
 
 
 
 
  
 
 
sxiao@bsd.uchicago.edu 
 
 
 
 
 
 
 
cfitzpat@bsd.uchicago.edu 
  
Interventional Radiologist:  
 
            Laboratory  Correlatives Coordinator: 
Paul Chang, MD 
 
  
 
 
Leah Chase 
University of Chicago Medical Center 
 
University of Chicago Medical Center 
Chicago, IL 60637 
 
  
 
 
Chicago, IL 60637 
Tel (773)  702-2456 
 
  
 
 
Pager 7918 
Fax (773) 834-8722  
  
 
 
lmchase@medicine.bsd.uchicago.edu 
pchang@radiology.bsd.uchicago.edu 
           rrendak@medicine.bsd.uchicago.edu 
 
Co-Investigator: 
 
  
 
 
  
Hedy Kinder, MD 
 
  
 
 
  
5841 S. Maryland Ave. MC2115 
 
 
  
Chicago, IL 60637 
 
 
 
 
  
Phone: 773-702-0360  
 
 
  
Email: hkindler@medicine.bsd.uchicago.edu 
  
 
 
 

2 
 
SCHEMA 
PANGEA-IMBBP:     Personalized ANtibodies for Gastro-Esophageal Adenocarcinoma-  
 
 
 
 
 
      A 1st Pilot Metastatic Trial of Biologics Beyond Progression  
Key Patient Eligibility Criteria:                                                               
See Section 3.1 for complete list of criteria.  
1. Histologically confirmed metastatic gastric or esophagogastric junction (type I,II,III Siewert) 
adenocarcinoma  
2. Newly-diagnosed chemo-naïve or recurrent after curative-intent surgery 
 
>6 months after completion of adjuvant therapy (including chemotherapy and/or radiotherapy) 
 
No prior treatment for stage IV disease with any targeted agent except trastuzumab/nivolumab 
    Patients who have started first line fluoropyrimidine/platinum therapy (+/-trastuzumab or 
nivolumab) may be considered for trial participation if they have received no more than 4 doses of 
therapy (5FU/LV bolus is optional with FOLFOX) at the time of consent and screening.- 
 
These patients will be required to meet ‘next cycle’ parameters for eligibility 
before commencing treatment on trial (as per Section 6) rather than being 
required to meet parameters as indicated below in #12 which is for previously 
untreated metastatic/recurrent patients. 
3. Measurable metastatic disease by RECIST 1.1 criteria,  
 
Must be amenable to ultrasound or CT-guided biopsy of one metastatic lesion or: 
 
Peritoneal disease as the sole site of occult metastasis or presenting as malignant ascites is 
acceptable if a cell block of tumor cells can be obtained showing >20% viable tumor cells. 
4. No currently active second malignancy 
5. No uncontrolled intercurrent illness or infection 
6. ECOG PS 0-2 
7. Age > 18 years 
8. No CVA within 6 months, no recent MI within 6 months 
9. Patients must have normal organ and marrow function as defined below: 
 
 
 
- 
granulocytes 
 
 
>1,500/mcL 
 
 
 
- 
platelets 
 
       > 100,000/mcL 
 
 
 
- 
total bilirubin 
 
 
< 1.5 x ULN, <1.8 x ULN with liver metastases and not  
 
 
 
 
 
 
 
             amenable to biliary stent 
 
 
 
- 
AST(SGOT)/ALT(SGPT)          
 
 
 
 
 
 
 
 
 
 
<2.5 X upper limit of normal without liver metastases; 
 
 
 
 
<5 X institutional upper limit of normal with liver metastases 
 
 
 
- 
creatinine 
 
 
within normal institutional limits (<1.5) 
OR 
 
 
 
- 
creatinine clearance  
        >50 mL/min/1.73m2 for creatinine level above normal 
 
 
 
-       INR  
 
 
 
 < 1.5      
        
10. Consent to baseline metastatic biopsy and biopsy at time of each progressive disease (of 
metastatic/progressing lesion) for enabling biomarker assessment and treatment assignment (at each 
time point – baseline, PD1, PD2, PD3) as well as for correlative studies.  
 Consent to baseline and serial blood draws for plasma/serum/whole blood banking for correlative 
studies 
11. Ability to understand and the willingness to sign a written informed consent document and consent to the 
serial nature of the proposed PANGEA treatment with first, second and third line therapy as tolerated. 
12. Ability to comply with requirements of the protocol, as assessed by the investigator and signing the 
consent form.  
13. If history of exposure to anthracyclines during perioperative treatment, the following cumulative doses of 
anthracyclines must be less than:  
Epirubicin  < 720 mg/m2  
Doxorubicin or liposomal doxorubicin < 360 mg/m2 
Mitoxantrone > 120 mg/m2 and idarubicin > 90 mg/m2  
If more than one anthracycline has been used, then the cumulative dose must not exceed the 
equivalent of 360 mg/m2 of doxorubicin.  
14. Cardiac Ejection Fraction >50% (for HER2+ patients) as assessed by echocardiogram, MUGA scan, or 
cardiac MRI  
15. Willingness to use effective and reliable methods of contraception. 
16. History of autoimmune disease (for MSI-H/EBV/PDL1>10CPS/TMB>15mts/Mb patients) documented by 
rheumatologist/specialist 
 

3 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
     FIGURE 1: PANGEA Trial Schema. 
1. 
Trastuzumab with 5FU plus a platinum is currently a standard treatment option for first line HER2+ metastatic disease, 
indicated in pink. Treatment for HER2+ patients will commence immediately upon obtaining results from routine clinical 
standard workup as well as biopsy of a metastatic site. (as in section 9.2), but this can be changed if the metastatic site is 
discordant or if a better treatment option (ie IO: MSI-High and/or EBV+ and/or TMB-high >15 mts/Mb and/or PDL1+ >10% 
CPS) is determined from their metastatic site 
2. 
HER2-negative patients will commence FOLFOX therapy alone until appropriate investigational biologic agents are 
determined and (or become) available. 
3. 
EGFRab = ABT806; VEGFR2ab = ramucirumab; METab* = pending; FGFR2ab = pending*; PD1-Ab = nivolumab.   
*patients may be able to receive anti-MET/FGFR2 antibodies on other studies, and if so, they will be followed for survival 
outcomes and other translational correlatives as per the PANGEA study, but treated according to protocol of the other 
specific study with the anti-MET or anti-FGFR2 antibodies.  
4. 
PD (progressive disease) will lead to a repeat biopsy of a progressing lesion, change of chemotherapy backbone, but 
continuation of assigned biologic.  
*However, if the tumor molecular category ‘drifts’ at any time point (PD1 or PD2) based on the new Biomarker Assessment 
and Treatment Algorithm (see Figure 3), then there will be a change of both     i) chemotherapy backbone and ii) to the 
appropriate biologic, and the previous biologic, if any, will be discontinued.  
5.  HER2++ incidence is ~15-20%, while MET++ incidence is ~8%. Approximately 20% will be EGFR++/+ (of which 
EGFR++ amp ~6%), and FGFR2++ 7%.  The ImmunoOncologic (IO) group includes MSI-high, and/or EBV+ and/or PDL1+ 
CPS>10% and/or High TMB >15mt/Mb tumors  
(together amounting to 15% of GEA) and the remainder will be in 
VEGFR2++/+ groups (See section 13.1 for statistical analysis for the primary efficacy endpoint). (see Figure 3) 

4 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
FIGURE 1: PANGEA Trial Schema. 
5. Traztuzumab with 5FU/platinum is currently standard treatment option for first line 
HER2+ metastastic disease, indicated in pink. Treatment for HER2+ patients will 
commence immediately upon obtaining results from routine clinical standard workup. 
6. HER2- patients will commence FOLFOX therapy immediately, and treatment with 
biologic will be added after 2 months of chemotherapy, in order to allow for ample time 
for tissue collection, biomarker assessment, and treatment assignment.  (see Figure 2) 
7. PD (progressive disease) will result in repeat biopsy of a progressing lesion, change of 
chemotherapy backbone, but continuation of assigned biologic.  
*However, if the tumor molecular category ‘drifts’ at any timepoint (PD1 or PD2) based 
on the Biomarker Assessment and Treatment Algorithm (see Figure 3), then there will  
be a change of both i) chemotherapy backbone and ii) to the appropriate biologic, and 
the previous biologic will be discontinued.  
FIGURE 2: PANGEA TREATMENT STRATEGY 
 
First Line:      mFOLFOX6  –    with appropriate Biologic 
Second Line: *FOLFIRI       –     with appropriate Biologic 
Third Line:     *FOLTAX        –     with appropriate Biologic 
 
*5FU-LV bolus and 5FU continuous infusion with irinotecan 
(second line) or docetaxel (third line) will continue as from 
mFOLFOX6, with any dose reductions/omissions from the prior 
line of therapy continued to the next line of therapy.  
FIGURE 2: PANGEA TREATMENT STRATEGY 
 
First Line:      mFOLFOX6  –    with appropriate Biologic 
Second Line: *FOLFIRI      –     with appropriate Biologic 
Third Line:     *FOLTAX      –      with appropriate Biologic 
 
*If the bolus 5FU is dropped for toxicity with any regimen, it should not 
be resumed with any subsequent regimen, and continuous 5FU doses 
once reduced are not to increase with subsequent regimens.  
** Patients will commence FOLFOX therapy alone until 
confirmation of their molecular profile.  FOLFOX alone will be 
continued per routine while molecular testing is conducted to 
allow for all testing and treatment assignment to be performed. 
When the biologic group is identified, the molecularly targeted 
agent is added at the next due cycle.  
 
 
 

5 
 
 
 
 
 
 
FIGURE 3:  PANGEA BIOMARKER ASSESSMENT & TREATMENT ALGORITHM 
The treatment assignment algorithm is derived as in Section 2.5. One notes various 
‘layers’ of positivity for a given molecular group – eg. Steps 3 and 7 are classified as EGFR 
(++ or +), and Step 6 and 8 are classified to VEGFR2 (++ or +). This is an attempt to 
stratify and group tumors using a prioritized scheme, based on best currently available 
evidence regarding driver biology, as well as availability of targeted agents. If assigned to 
a biomarker where drug is currently not available, patients will be treated with standard of 
care until such targeted therapy becomes available – see protocol details. 
Immunooncology (IO) therapy Group includes MSI-High and/or EBV+ and/or PDL1+ 
CPS>10% and/or High TMB >15mt/Mb tumors 
Genomic aberrations in RAS/RAF/MEK/ERK and/or PI3K/PTEN/mTOR/AKT and/or GNAS 
pathways receive anti-angiogenesis with anti-VEGFR2 antibody. 
 
 
 
 
 
 
 
 
 

6 
 
Figure 4: PANGEA Practical Flow 
 
 
 
 
 
 
 
 

7 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Figure 5: Demonstration of intra-patient and inter-patient tumor heterogeneity.  
A)  Intra-patient tumor heterogeneity in an individual patient through space (ordinate y-axis) from primary 
tumor to metastatic disease and over time (abscissa x-axis) through natural and treatment selection 
pressures.  
B) Intra-patient tumor heterogeneity with additional dimension of inter-patient heterogeneity on z-axis. 
Pink Bars: options for location of biopsy; pink arrows: biopsies at progression 
Proteomics 
B 
A 
B 

8 
 
 
 
 
 
 
 
 
 
Figure 6. PANGEA classification into main categories using the Biomarker and 
Treatment Algorithm (Figure 3). Although essentially every patient has a unique profile, 
even when considering genomics (A) or proteomics (B) alone, to be practical, PANGEA 
incorporates both genomic and proteomic profiles as a compromise between the potential 
(infinite) number of treatment categories and actual feasibility of conducting such a trial, to 
derive a set of major molecular categories (using the prioritization scheme in Figure 3). 
Proportions (C) represent a preliminary cohort of approximately 50 patients’ PANGEA 
classification. (++ = amplified, + = overexpressed non amplified) 
 
 
 
 
 
C 

9 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
PANGEA TABLE OF CONTENTS 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
             Page 
 
SCHEMA ................................................................................................................................ 1 
      Patient Eligibility ........................................................................................................ …2 
      Figure 1: Trial Schema……………………………………………………………………. .... 3 
      Figure 2: Treatment Strategy – mFOLFOX6FOLFIRIFOLTAX………..……....... .... .4 
      Figure 3: Biomarker Assessment and Treatment Algorithm…………….…...……….. .... 5 
      Figure 4: PANGEA Practical Flow……………………………………………………….. .... 6 
      Figure 5:  Demonstration of intra-patient and inter-patient tumor heterogeneity…… .... 7 
      Figure 6:  PANGEA classification into 6 main categories…………………………….. .... .8 
 
1. OBJECTIVES ................................................................................................................. 14 
1.1 
Primary Objectives ......................................................................................... 14 
1.2 
Secondary Exploratory Objectives ................................................................. 14 
1.3 
Laboratory/Translational Exploratory Objectives ........................................... 15 
 
2. BACKGROUND ............................................................................................................. 17 
2.1 
Gastroesophageal Cancer (GEC) .................................................................. 17 
2.1.1 
Epidemiology of GEC ..................................................................................... 17 
2.1.2 
Histologic Classification and etiology of GEC ................................................ 17 
2.1.3    
Prognosis ....................................................................................................... 17 
 
2.1.4    
First Line Systemic Treatment for Advanced/Metastatic GEC ....................... 18 
2.1.5 
 
Second Line and Third line Treatment ........................................................... 19 
2.1.6    
Chemotherapy Regimens for GEC ................................................................ 20 
2.1.6.1     5-Fluorouracil ................................................................................................. 20 
2.1.6.2     Oxaliplatin ....................................................................................................... 22 
 
2.1.6.2.1  mFOLFOX6 .................................................................................................... 23 
2.1.6.3     Irinotecan ........................................................................................................ 23 
2.1.6.3.1  FOLFIRI .......................................................................................................... 23 
2.1.6.4     Docetaxel ....................................................................................................... 23 
2.1.6.4.1  FOLTAX .......................................................................................................... 24 

10 
 
2.1.7 
HER2 positive GEC ........................................................................................ 25 
2.1.7.1 
HER2 Positivity in Advanced Gastric Cancer………………………………     25 
2.1.7.2 
Trastuzumab in the Treatment of Advanced GEC…………………………     26 
2.2 
Molecular Heterogeneity of GEC: Inter-Patient ............................................. 26 
2.3 
Molecular Heterogeneity of GEC: Intra-Patient ............................................. 28 
2.3.1 
Molecular Heterogeneity Through Space ...................................................... 28 
2.3.2 
Molecular Heterogeneity Through Time ......................................................... 28 
2.4 
Rationale of Mandatory Biopsies and Integral Biomarkers ............................ 28 
2.4.1 
Rationale of Biopsies and Personalized Approach at Baseline ..................... 29 
2.4.2 
Addressing Inter-Patient Heterogeneity ......................................................... 30 
2.4.3 
Addressing Intra-Patient Heterogeneity Through Space ............................... 30 
2.4.4 
Rationale of Serial Biopsy and Biologic Beyond Progression (BBP)  ............ 30 
2.4.4.1 
Addressing Intra-Patient Heterogeneity Through Time with Serial Biopsies…...    30 
2.4.4.2 
Rationale of Continuation of Biologic Agents Beyond Progression (BBP) …     31 
2.5 
   Biomarker Assessment and Treatment Algorithm .......................................... 31 
2.5.1      Rationale of Molecular Categories and Treatment Assignment .................... 31 
 2.5.1.1   HER2 .............................................................................................................. 32 
 2.5.1.2   MET  ............................................................................................................... 33 
2.5.1.3   EGFR  ............................................................................................................ 33 
2.5.1.4   FGFR2 ............................................................................................................ 34 
2.5.1.5 
MSI-H/EBV+/High TMB >15mt/Mb/PDL1+ CPS>10 ...................................... 34 
2.5.1.6 
KRAS/PIK3CA/AKT (“KRAS-like”: VEGFR2) ................................................. 34 
2.5.1.7 
Rationale of Prioritized Treatment Algorithm ................................................. 35 
2.5.2      Background of Biomarker Assessment Techniques…………………..……    37 
2.5.2.1  Fluorescence in Situ Hybridization (FISH)  .................................................... 39 
2.5.2.2 
Immunohistochemistry (IHC)  ........................................................................ 39 
2.5.2.3 
Mass Spectrometry (MS)  .............................................................................. 40 
2.5.2.4 
Next-Generation Sequencing (NGS)  ............................................................ 41 
2.5.2.5 
ctDNA NGS .................................................................................................... 41 
2.6 
 
Investigational Biologic Therapies ................................................................. 41 
2.6.1 
Personalized Approach: Treating Oncogenic Drivers .................................... 41 
2.6.2 
HER2: (Trastuzumab) .................................................................................... 41 
2.6.3 
MET: (TBD)..................................................................................................... 42 
2.6.4 EGFR: ( ABT-806) .......................................................................................... 42 
2.6.5 
FGFR2 (TBD) ................................................................................................. 42 
2.6.6 RAS/PIK3CA/GNAS ( Ramucirumab) ............................................................ 42 
2.6.7 
MSI-H/EBV+/TMB-High>15mt-Mb/PDL1+ CPS>10% (nivolumab)  .............. 42 
 
3. PATIENT SELECTION ................................................................................................... 43 
3.1 
 
Eligibility Criteria  ............................................................................................ 43 
3.2 
 
Inclusion of Women and Minorities ................................................................ 44 
 
4. REGISTRATION PROCEDURES .................................................................................. 45 

11 
 
4.1  
 
General Guidelines ........................................................................................ 45 
4.2  
 
Registration Process & Data Submission for Consortium Affiliates .... ………45 
4.3  
 
Data and Safety Monitoring………………..…………..…… ………….…… .... 45 
 
 
5. TREATMENT PLAN ....................................................................................................... 46 
5.1  
 
Agent Administration and use of palliative therapy (ie Radiation)………. ..... 46 
5.1.1    
Safety Lead-In ................................................................................................ 46 
5.1.2    
Treatment Strategy: PANGEA ........................................................................ 47 
5.1.3    
mFOLFOX6 .................................................................................................... 48 
5.1.4     
FOLFIRI .......................................................................................................... 50 
5.1.5     
FOLTAX .......................................................................................................... 51 
5.1.6  
HER2: Trastuzumab  (Herceptin) ................................................................... 52 
5.1.7  
MET: TBD  ...................................................................................................... 53 
5.1.8  
EGFR:ABT806 ............................................................................................... 54 
5.1.9  
FGFR2: TBD .................................................................................................. 54 
5.1.10  
MSI-H/EBV+/High TMB >15mt/Mb PDL1+ CPS>10: nivolumab ................... 54 
5.1.11  
VEGFR2:  ramucirumab ................................................................................. 54 
5.2  
 
General Concomitant Medication and Supportive Care Guidelines .............. 54 
5.2.1 
Antiemetics ..................................................................................................... 54 
5.2.2 
Growth Factors ............................................................................................... 54 
5.2.3 
Central Access Device ................................................................................... 54 
5.3 
Duration of Therapy on Trial........................................................................... 54 
5.4       
Duration of Follow Up ..................................................................................... 54 
 
6. DOSING DELAYS/DOSE MODIFICATIONS……………………………….………….. .... 55 
      6.1        5-FU/Leucovorin……………………………………………………….……… .... 55 
      6.2        Oxaliplatin…..………………………………………………………...….…….. .... 57 
      6.3        Irinotecan………………………………………………..……………….…….. .... 57 
      6.4        Docetaxel …..………………………………………………………..….….….. ... 57 
      6.5        Trastuzumab …..………………………………………………….…….…….. ... .61 
      6.6        FGFR2 antibody TBD…………………………………………….…..…...…... ... 63 
      6.7  
 ABT-806….………………………………………….…..…...….........................64 
      6.8  
Ramucirumab …………………………………….…..…...….........................64 
      6.9 
Nivolumab…………………………………………………….…..…...…... .......... 64 
 
 6.10        MET Antibody TBD………………………………………………….…..…...…... 64 
 
7. ADVERSE EVENTS:  LIST AND REPORTING REQUIREMENTS .............................. 65 
7.1  
  
Adverse Events Characteristics ..................................................................... 65 
7.2  
  
Adverse Event Definitions .............................................................................. 65 
7.2.1     
Adverse Event ................................................................................................ 65 
7.2.2     
Serious Adverse Events ................................................................................. 66 
7.2.3     
Unexpected Events ........................................................................................ 66 
7.2.4     
Adverse Reactions ......................................................................................... 67 

12 
 
7.3  
     Reporting Procedures for Serious Adverse Events ....................................... 67 
7.3.1  
Routine Adverse Event Reporting .................................................................. 67 
7.3.2  
Serious Adverse Event Reporting .................................................................. 68 
 
8. PHARMACEUTICAL INFORMATION ........................................................................... 69 
8.1  
Biologic Agents ............................................................................................... 69 
8.1.1  
HER2: Trastuzumab  (Herceptin) ................................................................... 69 
8.1.2  
MET: TBD  ...................................................................................................... 69 
8.1.3  
EGFR:ABT806 ............................................................................................... 69 
8.1.4  
FGFR2: TBD .................................................................................................. 69 
8.1.5  
MSI-H/EBV+/High TMB >15mt/Mb PDL1+ CPS>10: nivolumab ................... 69 
8.1.6  
VEGFR2: Ramucirumab ................................................................................ 69 
8.2      
Commercial Cytotoxic Agents ........................................................................ 69 
8.2.1     
5-Fluorouracil/leucovorin ................................................................................ 69 
8.2.2     
Oxaliplatin ....................................................................................................... 69 
8.2.3     
Irinotecan ........................................................................................................ 69 
8.2.4     
Docetaxel ....................................................................................................... 69 
 
9. BIOMARKER ASSESSMENT METHODS .................................................................... 70 
9.1 
Background and Algorithm ............................................................................. 70 
9.2  
Tissue Biomarker Assessment Methods ........................................................ 70 
 9.2.1      Fluorescence in situ hybridization (FISH) ...................................................... 71 
 9.2.1.1   HER2  ............................................................................................................. 71 
 9.2.1.2   MET  ............................................................................................................. 71 
 9.2.1.3   FGFR2 ............................................................................................................ 71 
 9.2.1.4   RAS  ............................................................................................................. 71 
 9.2.1.5   MSI-H/EBV+/High TMB >15mt/Mb PDL1+ CPS>10: nivolumab ................... 71 
9.3.1.6     EGFR  ............................................................................................................. 71 
 9.2.2  
Next-Generation Sequencing: Foundation One and Guardant360 ............... 72 
9.2.3  
Immunohistochemistry ................................................................................... 72 
 9.2.3.1   HER2 .............................................................................................................. 72 
 9.2.3.2   MET ................................................................................................................ 72 
9.2.4   
Mass Spectrometry: GEC-plex ...................................................................... 72 
9.2.5      Collection, Handling, and Shipping of Specimens ......................................... 72 
 9.3 
Blood Banking ................................................................................................ 74 
 9.3.1      Collection of Specimens................................................................................. 74 
 9.3.2      Handling of Specimens .................................................................................. 75 
     9.4 
   Shipping of Specimens……………………………………………………….   ... 75 
 
10. STUDY CALENDAR……………………………………………………………………..   ... 76 
 
11.  MEASUREMENT OF EFFECT………………………………………………………….   .. 78 
11.1 
Antitumor Effect – Solid Tumors .......................................................... ……..78 

13 
 
11.1.1 
Definitions ....................................................................................................... 78 
11.1.2 
Disease Parameters ....................................................................................... 78 
11.1.3 
Methods for Evaluation of Measurable Disease ............................................ 79 
11.1.4 
Response Criteria .......................................................................................... 80 
11.1.4.1  Evaluation of Target Lesions…………………………………………………. .... 80 
11.1.4.2  Evaluation of Non-Target Lesions…………………………………………… .... 81 
11.1.4.3  Evaluation of Best Overall Response……………………………………….. .... 81 
11.1.5 
Duration of Response .................................................................................... 82 
11.1.6 
Progression-Free Survival ............................................................................. 82 
11.1.7 
Response Review .......................................................................................... 83 
11.2 
Other Response Parameters ......................................................................... 83 
 
11.2.1    Overall Survival .............................................................................................. 83 
 
11.2.2    Toxicity ............................................................................................................ 83 
 
11.2.3    Safety ............................................................................................................. 83 
 
11.2.4    Feasibility………………………………………………………………………. .... 83 
 
12. DATA SAFETY REVIEW………………………………………………………………... ..... 84 
13. STATISTICAL CONSIDERATIONS ............................................................................... 84 
 
13.1 
Study Design/Endpoints ................................................................................. 84 
 
13.2 
Sample Size/Accrual Rate ............................................................................. 85 
 
13.3 
Analysis of Secondary Endpoints .................................................................. 85 
 
13.3.1   
Secondary Endpoints ..................................................................................... 85 
 
13.3.2   
Subset analyses between and within molecular categories .......................... 85 
 
13.4  
Reporting and Exclusions .............................................................................. 86 
 
13.4.1 
Evaluation of toxicity ...................................................................................... 86 
 
13.4.2 
Evaluation of response................................................................................... 86 
 
14. REFERENCES .............................................................................................................. 88 
 
Appendix A: Blood Sample Collection Form ................................................................. 97 
Appendix B: Acceptable and Unacceptable Forms of Contraception for Women of 
Childbearing Potential …………………………………………………………………….    98 
Appendix C:  Collection of Tissue Specimens Algorithm…..…………………………….99 
 
TABLES: 
 
 
Table 1: Molecular inter-patient heterogeneity of GEC, examples……………………...36 
 
Table 2: Treatment assignment examples based on molecular profile, examples........37 
 
Table 3: 5-FU Dose Modifications for Non-Hematologic Toxicities……………………...56 
 
Table 4: Dose Adjustment Levels for Any Toxicities for Cytotoxics…..………………...57 
 
Table 5: Hematologic Dose Reductions……………………………………………….…...58 
 
Table 6: Non-Hematologic (except Neurotoxicity) Dose Reductions………………….. 59 
 
Table 7: Dose Modifications for Oxaliplatin or Docetaxel Induced Neurotoxicity….     60 
 
 

14 
 
1. OBJECTIVES 
 
1.1  Primary Objectives 
 
1.1.1 To determine the safety and feasibility of obtaining baseline biopsies of 
metastatic disease sites (liver, lung, lymph node, peritoneum/ 
carcinomatosis) for molecular testing, in order to proceed with the biomarker 
assessment and treatment assignment algorithm (Figure 3,4,6).  
 
1.1.2 To determine the safety and feasibility of obtaining serial biopsies of 
progressing metastatic disease sites (liver, lung, lymph node, 
peritoneum/carcinomatosis) for molecular testing at each progression point 
(PD1,2,3 – Figure 1,2,4,6), in order to proceed with the biomarker 
assessment and treatment assignment algorithm (Figure 3), as assessed by 
rate of successful treatment category assignment. 
 
1.1.3 To determine the median overall survival (mOS) of the combined HER2++, 
MET++, EGFR++/+, MSI-H/EBV+/TMB-High>15mt-Mb/PDL1+ CPS>10%, 
FGFR2++, and VEGFR2++/+ groups (N=68 total treated per intented protocol 
with targeted therapies) treated with their respective targeted therapies per 
the treatment assignment algorithm (intention to treat), with each line of 
cytotoxic chemotherapy (up to three lines, Biologic Beyond Progression), 
compared to historical controls having an aggregate mOS of approximately 
12 months.  
 
1.2  Secondary Exploratory Objectives  
 
 
1.2.1  To determine the median overall survival (mOS) collectively of all patients 
undergoing tumor molecular profiling with classification into one of six 
predefined gastroesophageal cancer (GEC) ‘oncogenic driver’ categories 
(HER2++, MET++, EGFR++/+, FGFR2++, MSI-H/EBV+/TMB-High>15mt-
Mb/PDL1+ CPS>10%, VEGFR2++/+) with paired specific targeted therapy 
via the biomarker assessment and treatment algorithm (Figure 3), along 
with standard chemotherapy (up to 3 lines), compared to historical controls 
having an aggregate mOS of approximately 12 months. (Figure 1,2)  
 
1.2.2  To determine the median progression free survival (mPFS1) of first-line 
chemotherapy (mFOLFOX6) plus ‘personalized’ treatment of trastuzumab 
for HER2+ compared to historical controls of mPFS1 of approximately 6 
months. (Figure 1,2) 
 
1.2.3 To determine the median progression free survival (mPFS1) of standard care 
with first-line chemotherapy (mFOLFOX6) plus ‘personalized’ treatment, 
compared to historical controls of mPFS1 of approximately 5 months for all 
patients in all five molecular categories. (Figure 1,2) 
 
1.2.4 To determine the rate of continuing with a second-line and third-line 
treatment (chemotherapy backbone FOLFIRI, FOLTAX), compared to 
historical controls (50%, 25%); to determine the rate and type of further 
treatments off-protocol after completion of third line therapy. (Figure 1) 
 

15 
 
1.2.5 To determine the mPFS2,3 of continuation of the re-targeted molecular 
therapy (Biologic Beyond Progression- BBP) along with the second and 
third line chemotherapy, compared to historical controls of mPFS2 (of 
approximately 4 months) and mPFS3 (of approximately 2 months) with 
chemotherapy alone. (Figure 1,2). (mPFS2 denotes the median time to 
second disease progression after progressing on first-line therapy; mPFS3 
denotes the median time to third disease progression, after progressing on 
second-line therapy.) 
 
1.2.6 To determine the 6 month, 12 month, 18 month and 24 month survival rate, 
compared to historical controls. 
 
1.2.7 To determine the overall response rate (ORR) at each line of therapy 
(ORR1,2,3), compared to historical controls (ORR1 30%, ORR2 20%, ORR3 
10%).  
 
1.2.8 To determine the mPFS1+2, mPFS1+2+3.  
 
1.2.9 To determine the disease control rate (DCR) at each line of therapy 
(DCR1,2,3). 
 
1.2.10 To determine the toxicity experienced by GEC patients treated with the 
combination of serial mFOLFOX6 FOLFIRI  FOLTAX plus assigned 
biologic treatment with each line of therapy.   
 
 
1.3  Laboratory/Translational Exploratory Correlatives Objectives 
 
1.3.1 To determine and refine our understanding of inter-patient GEC tumor 
heterogeneity by evaluating genomic and proteomic tumor profiles in 
all patients on trial. 
 
1.3.1.1 To determine the somatic genomic changes of 315 actionable cancer-
related genes (mutation, amplification, and translocation), MSI-status/IO, 
and 27 genes with common translocations, using targeted deep next-
generation sequencing (NGS), as well as fluorescence in situ 
hybridization (FISH) for HER2, MET, FGFR2, EGFR, KRAS. 
 
1.3.1.2 To determine the expression of known oncogenic GEC drivers including 
HER2, MET, FGFR2, EGFR, KRAS using i) a novel GEC-multiplexed 
selected reaction monitoring mass spectrometry (containing 20 
oncoproteins) and ii) immunohistochemistry (IHC). 
 
1.3.1.3 To determine the relationship of these parameters in 1.3.1.(1-2) to clinical 
outcomes including mPFS, DCR, ORR, mOS, and clinical factors 
including ethnicity, tumor differentiation, histology, primary anatomical 
location, and stage. 
 
1.3.2  To determine and refine our understanding of intra-patient GEC tumor 
heterogeneity through space and time, by evaluating genomic and 
proteomic profiles of each tumor in all patients on trial. 
 

16 
 
1.3.2.1 To determine the rate of baseline (prior to therapy) tumor molecular 
evolution from primary tumor to metastatic lesion (intra-patient 
heterogeneity through space) by comparing genomic changes (mutation, 
amplification, and translocation) using i) NGS (and FISH), ii) proteomic 
changes by GEC-plex mass spectrometry and IHC, and iii) kinase activity 
with PamGene iv) ctDNA sequencing results 
 
1.3.2.2 To determine the rate of tumor molecular category migration at baseline 
within the Biomarker and Treatment Algorithm (6 category Classification, 
see Figure 6) comparing primary tumor to metastatic disease.  
 
1.3.2.3 To determine tumor molecular evolution over time (intra-patient 
heterogeneity through time/treatment) from baseline to first progression 
(PD1) and subsequent progressions (PD2, PD3) for those receiving 
second/third line therapy, assessing for genomic/proteomic evolution. 
 
1.3.2.4 To determine the rate of new/loss of molecular aberrations at each 
progression point (PD1,2,3) 
 
1.3.2.5 To determine the rate of molecular category migration within the 
Biomarker and Treatment Algorithm ( see Figure 6) at each progression 
point (PD1,2,3). 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

17 
 
 
2. BACKGROUND 
 
2.1  Gastroesophageal cancer (GEC):  
Adenocarcinoma of the stomach and esophagogastric junction (EGJ)  
 
2.1.1 Epidemiology of gastroesophageal adenocarcinoma (GEC) 
 
Gastroesophageal cancer (GEC) represents a challenging global health 
problem. GEC is the fourth most common malignancy behind lung, breast, and 
colorectal cancers, with approximately 1 million cases per year occurring around 
the world. GEC is the second leading cause of cancer death globally and it is 
estimated that in excess of 700,000 patients will die from the disease annually.1-4 
There are significant geographic variations in the incidence of GEC; it is more 
common in East Asia, Eastern Europe, and parts of Central and South America 
than it is in the United States or Western Europe.  Almost 70% of cases arise in 
developing countries with approximately 40% of cases occurring in China alone. 
There are clear epidemiologic differences between cancer localized to the 
proximal stomach (gastric cardia type III esophagogastric juntion (EGJ)) along 
with other EGJ (Type I,II) in contrast to those that are localized to the rest of the 
stomach (distal gastric cancer (GC)).5  Cancer of the cardia accounts for 39% of 
GEC cases in Caucasian men in the United States but only in 4% of GEC in 
men in Japan. For reasons that are not clear, cancer of the gastric cardia and 
lower esophagus (EGJ) has increased rapidly in developed countries since the 
1970s.5 
 
2.1.2 Histologic Classification and Etiology of GEC  
 
The histology of GEC falls into two broad subtypes based on microscopic 
features observed in gastric tumors, namely intestinal or diffuse, according to 
Lauren’s classification.6 Intestinal-type tumors tend to arise in the antrum or 
antral-corpus junction. Intestinal-type cancers are classically characterized by 
glandular differentiation on a background of gastric atrophy or intestinal 
metaplasia, whereas diffuse cancers typically appear as rows of single 
mononuclear “signet ring” cells with little cell adhesion.5,7 These apparently 
distinct features, however, are not always discernible in clinical samples, where 
inter-observer variation and unclassifiable or “mixed” subtypes are not 
uncommonly reported. Intestinal-type tumors are significantly more common 
than the diffuse type and tend to be associated with intestinal metaplasia and 
chronic inflammation (e.g. atrophic gastritis), often as a result of chronic 
Helicobacter pylori infection. By contrast, diffuse tumors do not generally 
develop on a background of intestinal metaplasia and inflammation is 
characteristically absent.7  
 
2.1.3 Prognosis 
 
Survival rates from GEC have improved over the last few decades. Five-year 
overall survival (OS) in the Western world is estimated at ~20%.8 In the West, 
fewer patients are referred for surgery compared with Asia, but those who 
undergo resection have a higher survival rate, which reaches 50%, possibly due 
to more accurate preoperative staging and improved imaging techniques. In 
large-scale screening programs in Asia, detection at earlier stages and more 

18 
 
aggressive surgical approaches, including more frequent D2 lymph node 
resection, contribute to higher OS rates of ~60%. The median OS among 
patients with late-stage GEC is approximately 14 months in patients with locally 
advanced disease and 9-12 months in patients with metastatic disease.9,10  
 
2.1.4 First Line Systemic Treatment for Advanced/Metastatic GEC 
Active chemotherapeutics: 
 fluoropyrimidine, platinum, topoisomerase-1 inhibitor, taxane 
 
For patients with unresectable, metastatic disease, the main therapeutic option 
is chemotherapy. First line chemotherapy has been shown to increase survival 
and quality of life in patients with advanced GEC in several randomized trials 
and meta-analyses.11,12 It is evident that combination therapy outperforms 
single-agent (mainly 5-fluorouracil [5-FU]) therapy (hazard ratio [HR] = 0.83; 
95% CI: 0.74, 0.93).13 Median survival for patients with metastatic disease 
treated with chemotherapy ranges, depending on the sited reference and the 
time period of the clinical trial, from 8–13.9 months. A recent clinical trial with 
mFOLFOX6 chemotherapy reported a median OS of 13.9 months in a placebo 
arm (N=64) of a 124 patient trial.10 Increased estimates of mOS in recent trials 
compared to trials reported more than 5 years ago are likely due to improved 
best supportive care (BSC) as well as increasing numbers of patients 
proceeding to second and third line therapies (see Second and Third line 
Therapy, below). However, given that these recent numbers are from 
smaller phase II trials, our most robust estimates for median OS is 
approximately 9-12 months based on large phase III trials, which is why we 
chose 12 months for our historical control arm.    
 
Despite intensive evaluation of multiple chemotherapy regimens, no 
international consensus exists regarding the optimal first-line regimen in 
advanced GEC.  In Western countries and in Asia, the reference chemotherapy 
regimen for the first-line treatment of metastatic GEC is a fluoropyrimidine (5-FU 
or capecitabine) in combination with a platinum agent (either cisplatin or 
oxaliplatin) with or without a third cytotoxic drug (usually epirubicin or 
docetaxel).8  Based on several Phase III studies and meta-analyses, oxaliplatin 
and capecitabine have both been shown to be non-inferior to cisplatin and 5-FU, 
respectively 8,14-16 National Comprehensive Cancer Network (NCCN) and 
European Society for Medical Oncology (ESMO) guidelines recommend that a 
fluoropyrimidine (either 5-FU or capecitabine) combined with either cisplatin or 
oxaliplatin are appropriate standards of care in the first-line setting.  The use of 
irinotecan (topoisomerase-1 inhibitor) is usually reserved for second/third line, 
however, one first line trial evaluating S1/irinotecan showed a non-significantly 
improved mOS from 10.5 to 12.8 (p=0.23), but did have a significantly improved 
ORR1 from 26.9% to 41.5%, compared to S1 oral chemotherapy alone.17 
Recently another trial with FOLFIRI showed no difference with ECX therapy with 
mOS: 9.7 vs 9.5, respectively, and therefore is an option for first line therapy.18 
 
The use of three-drug “triplet” chemotherapy remains controversial, and usually 
is reserved for patients with very good performance status (PS – ECOG 0). The 
addition of a taxane or an anthracycline to a platinum-based doublet may be 
associated with an incremental improvement in survival of ~1 month for patients 
with metastatic GEC;13 however, this marginal survival benefit is counter-
balanced by significant treatment-associated toxicity8. Triplet regimens such as 

19 
 
docetaxel, cisplatin, and 5-FU (DCF); epirubicin, cisplatin, and 5-FU (ECF); or 
epirubicin, oxaliplatin, and capecitabine (EOX) are considered appropriate for 
highly functioning patients with minimal comorbidities,19 but their systematic use 
has not been widely recommended.8  Additionally, clinical trials are evaluating 
mFOLFIRINOX (5FU, irinotecan, and oxaliplatin) in the first line setting at the 
University of Chicago(NCT01643499).   
 
However, given the ease of use of mFOLFOX6 and the familiarity of this 
regimen in more common malignancies (ie colorectal cancer), mFOLFOX6 has 
become a standard first line treatment option for GEC both on or off clinical 
trials.10 Moreover, this reserves other drug classes (including taxanes and 
topoisomerase-1 inhibitors) for second/third line treatments in a tandem strategy. 
Furthermore, it is easier from a toxicity standpoint to add an investigational 
targeted agent to a doublet cytotoxic regimen versus a triplet cytotoxic regimen. 
Dropping the 5FU/LV bolus can limit toxicity without detriment in efficacy, and 
treating physicians may opt to use or not depending on the clinical 
circumstance. 
 
2.1.5 Second and Third Line Systemic Treatment for Advanced/Metastatic 
GEC 
 
Second Line: 
 
For patients who progress on front-line therapy, second-line therapy with 
irinotecan (or an irinotecan-containing regimen) or a taxane is recommended 
(NCCN category 2B).  
 
Single agent irinotecan in the second line setting has been investigated in 
several small trials.  One revealed a mOS of 4 months and mPFS of 2.6 months.  
The activity of irinotecan when used in combination with 5-fluorouracil and 
leucovorin (FOLFIRI) demonstrated a range of ORR2  of 3-29%, median PFS2 of 
2.3-4 months and median OS2 of 5.1-7.6 months and DCR2 of 29-63%.20-24 
 
Single agent taxane in the second line setting was evaluated in 49 patients and 
resulted in mOS 8.3 months, mPFS 2.5 months, and ORR 16.3%.25 More 
recently, the relatively large (N=168 84:84) phase III Cougar-02 trial comparing 
docetaxel to best supportive care (BSC) resulted in improved mOS from 3.6 to 
5.2 (p=0.01, HR 0.67), and RR2 7% and disease stabilization (SD) rate of 46% 
for a total DCR2  rate of 53%.26   
 
Comparing irinotecan to docetaxel in the second line setting, a three-arm trial 
including a BSC arm revealed no difference between the two chemotherapy 
arms (6.5 versus 5.2 months, respectively), but both cytotoxics significantly 
improved over BSC of 3.8 months.27 
 
Two studies evaluated the combination of docetaxel and irinotecan in the 
second line setting of GEC, one revealing 3 patients with complete response 
(CR) and 7 patients with partial response (PR) resulting in an ORR2 of 20.4%.28  
Another, showed a mOS2 of 4 months, and mPFS2 of 2.8 months.29 A meta-
analysis of 34 second line therapy trials (monotherapy (8), combined (17), and 
targeted (6))  revealed a wide range of outcomes: mOS2 4-11.4 months; mPFS2, 
RR 0-63%.30  

20 
 
Third Line: 
 
Few third line clinical trials have been performed, but a recent large 158 patient 
trial using FOLFIRI (after platinum, 5FU, taxane) in the third line revealed an 
ORR3 9.6%, mPFS3 2.1 months and mOS 5.6 months and DCR3 39.7%.31   
 
Finally, a clinical trial evaluating the sequence of second/third line use of 
FOLFIRI vs docetaxel/5FU (DF=FOLTAX) after failure of first line mFOLFOX6, 
revealed no difference in mOS between the two sequences; mOS was 16 
months.32 Again, this is a smaller trial and done in Asia, where mOS is better 
than in Western countries; the 12 month mOS is more representative of our 
intended patient population. 
 
Given the above, it is common practice for patients with preserved ECOG PS 
(<2) to continue with palliative second and third line therapy (irinotecan, 
docetaxel in either order) without or with the addition of continued 5-FU with the 
intention to achieve synergistic activity (FOLFIRI, FOLTAX = DF).    
 
No immunotherapy checkpoint inhibitors have been approved to date for 
patients with GEC in first line of therapy, however promising results have been 
reported in PDL1+ patients by IHC and now approved for third line or higher 
monotherapy in PDL1+ patients, and most importantly MSI-H patients as 
monotherapy in second or higher, which accounts for <5% of stage IV GEC. 
However, when randomized to getting control chemotherapy versus 
monotherapy checkpoint inhitibitor, these studies have been negative in both the 
second and third line setting, making it quite reasonable to continue with 
PANGEA treatments FOLFOXFOLFIRIFOLTAX plus appropriate biologic 
currently.  However, a recent study (Keynote 061) did demonstrate that patients 
with PDL1+ CPS (combined positivity score) >10% had survival benefit 
compared to chemotherapy in second line or higher (Fuchs et al. J Clin Oncol 
36, 2018 (suppl; abstr 4062)).  
 
2.1.6 Chemotherapy Regimens for GEC 
 
In advanced GEC, 5-fluoruracil has been the cornerstone of chemotherapy 
regimens and as a single agent results in response rates (RR1) of 15-30% 
alone.33,34 Numerous studies have shown that when 5-fluorouracil is combined 
with other cytotoxics, there is a significant improvement in response rate and 
time to progression at the expense of mildly increased and acceptable toxicity.34 
Historically, the most commonly used agents in advanced gastric cancer are a 
combination of cisplatin and 5-fluorouracil. While epirubicin is often added to this 
combination in Europe, there is no convincing evidence of its additional value in 
terms of improved survival or quality of life.35  The substitution of oxaliplatin for 
cisplatin has been shown to be non-inferior in terms of overall survival, with 
significantly less grade 3 and 4 neutropenia, nephrotoxicity, emetogenesis, and 
alopecia.14,15 Studies using combined 5-fluorouracil and oxaliplatin have 
demonstrated similar outcomes when compared to other reference regimens in 
advanced GEC.14,36,37 Notably, the addition of docetaxel to cisplatin and 5-
flurouracil (DCF) has demonstrated a marginally improved overall survival in 
advanced gastric cancer patients (9.2 vs 8.6 months).38 However, there is 
significantly more grade 3 and 4 neutropenia, complicated neutropenia, diarrhea 
and neurosensory toxicity, making this combination regimen suitable for only a 

21 
 
carefully selected patient population treated by physicians familiar with its 
administration.  Combination of 5FU with irinotecan (FOLFIRI) or docetaxel 
(DF=FOLTAX) are well established regimens, most often used for GEC in the 
second/third line settings, in any sequence.32  
 
2.1.6.1 
5-Fluorouracil  
 
5-fluorouracil (5-FU) acts as false pyrimidine or antimetabolite to ultimately 
inhibit the formation of the DNA-specific nucleoside base thymidine. The agent 
appears to successfully compete for the enzyme thymidylate synthase by 
displacing natural substrate uracil deoxyribonucleotide. 5-fluorouracil, thus, is 
similarly handled as the normal uracil substrate for activity when it is first 
converted enzymatically through several steps to the ribonucleoside and 
ribonucleotide. This ultimate metabolite can then bind selectively with the target 
enzyme and inhibit the formation of thymidine, an essential substrate for DNA 
synthesis. RNA synthesis is also affected to a lesser degree by inhibiting the 
utilization of preformed uracil. 5-FU is cell cycle phase specific agent with 
cytotoxic effects seen mainly in S-phase.  The two main routes of fluorouracil 
metabolism in man are intracellular activation to the active nucleoside and 
enzymatic destruction in the liver due to dihydro 5-FU dehydrogenase with 
ultimate conversion to inactive metabolites: CO2, urea, fluoro-B-alanine, and 
ammonia. The degradative enzymes are diffusely distributed and are found in 
the gastro-intestinal epithelium but apparently not in some colonic carcinoma. 
After a rapid intravenous injection of 15 mg/kg, peak plasma levels of 10-3 – 10-4 
are achieved. Primary half-life is 8-14 minutes. Plasma levels then decrease 
rapidly and are undetectable after 1 hour. The distribution volume is 25-33% at 
body weight. Up to 80% of a dose is detoxified via metabolic degradation in the 
liver, with significant renal excretion occurring after the first few hours. 
Ultimately, from 60 to 80 of radio-labeled carbon from a given dose is excreted 
through the lungs as carbon dioxide, however, less than 10% of unchanged drug 
is excreted by the kidneys with 90% during the first hour. Depressed renal 
function then does not require dosage adjustment for 5-FU. Clarkson et al found 
that when given as a continuous infusion (40-60 mg/kg/24 hour)39, stable plasma 
levels are obtained and less intact drug appears in the urine. This could indicate 
either more complete degradation to inactive metabolites or enhanced 
conversion to the active nucleoside. Fluorouracil distributes to all areas of body 
water apparently by simple diffusion. Thus significant quantities of drug may 
enter the CNS and after 15 mg/kg IV; cerebrospinal fluid levels of 6-8 x 10-6 M 
are obtained after 30 minutes. These levels persist for several hours and slowly 
subside. Although distribution to brain tissue is less rapid, abnormal areas such 
as those with neoplasms may take up the drug more readily. Intracarotid and 
intrathecal administration have led to augmented formation of neurotoxic 
metabolites fluoroacetate and fluorocitrate, and are therefore not recommended. 
Fluorouracil achieves high and persistent levels in effusions after intravenous 
administration.  
 
The spectrum of toxicity associated with 5-FU varies according to dose, 
schedule, and route of administration. On a particular schedule, considerable 
variation in the incidence and severity of these toxicities among patients is 
observed. The IV bolus schedule may result in severe gastrointestinal toxicity 
and may be life threatening. These toxicities include mainly mucositis and 
diarrhea. In some cases, disruption of the integrity of the gut lining may permit 

22 
 
access of enteric organisms into the bloodstream and potential overwhelming 
sepsis, particularly if the nadir coincides with diarrhea. In addition to dose 
limiting mucositis and diarrhea, IV bolus daily for 5 days can also result in 
granulocytopenia. With continuous infusion 5-FU, mucositis is usually dose 
limiting although diarrhea and dermatitis occur. Myelosuppression is generally 
mild to moderate in severity. High doses of 5-FU over a 24-hour period may 
have dose limiting gastrointestinal toxicity and neurotoxicity. A prolonged 
continuous infusion of low dose 5-FU can potentially have dose limiting 
mucositis and palmo-plantar erythrodysesthsia while diarrhea is less common. 
5-FU is the most extensively studied single agent in gastric carcinoma. An 
overall response rate of 21% has been reported. Infusional 5-FU is of interest 
given the drug’s short plasma half-life and because a much higher dose density 
can be achieved compared with bolus injections. 5-FU has an established 
efficacy in the treatment of advanced colorectal cancer for the last 40 years. A 
wide variety of regimens of 5-FU with or without folinic acid (FA) are in current 
use.  
 
The use of FA (folinic acid – leucovorin (LV)) bolus (400mg/m2 over 2 hours) 
followed by 5-FU with both bolus (400mg/m2 over) and continuous infusion (2.4-
3g/m2 over 46 hours) has become a common regimen, either alone or in 
combination with other cytotoxics oxaliplatin, irinotecan and docetaxel 
(mFOLFOX6, FOLFIRI, or FOLTAX).40  
 
2.1.6.2 
Oxaliplatin 
 
Oxaliplatin (Eloxatin) (trans-l-1,2-diaminocyclohexane oxalatoplatinum) is an 
antineoplastic platinum derivative with a 1,2-diaminocyclohexane [DACH] carrier 
ligand. Although the precise mechanism of action is unknown, platinum 
compounds are thought to exert their cytotoxic effects through the formation of 
DNA adducts that block both DNA replication and transcription. Like cisplatin, 
oxaliplatin reacts with DNA, forming mainly platinated intra-strand links with two 
adjacent guanines or a guanine adjacent to an adenine.41-43 However, DACH-
platinum adducts formed by oxaliplatin are apparently more effective at inhibiting 
DNA synthesis and are more cytotoxic than cis-diamine-platinum adducts 
formed from cisplatin and carboplatin.43-45 
 
The safety profile of oxaliplatin was evaluated in a phase I intra-patient 
escalation study of 44 patients with advanced cancer, who received 116 courses 
of oxaliplatin through seven levels, from 45 mg/m2 to 200 mg/m2 every four 
weeks. Oxaliplatin was administered without pre-hydration or post-hydration. 
Initially, all patients experienced nausea and vomiting. As a result, systematic 
pretreatment with antiemetics was given to all patients receiving >90 mg/m2 
oxaliplatin, which reduced Grade 3 or 4 nausea and vomiting to 11%. Diarrhea 
was mild (primarily Grade 1 or 2 in 24% of therapy courses). Hematologic 
toxicity was moderate. Grade 1 or 2 thrombocytopenia was dose related and 
occurred in 13% of patients receiving from 135 to 150 mg/m2, and 28.5% of 
patients receiving 175 to 200 mg/m2. Similarly, only Grade 1 or 2 neutropenia 
was observed, and hemoglobin levels remained unchanged. The dose-limiting 
side-effect of oxaliplatin therapy was a transient peripheral neuropathy. This 
toxicity usually appeared at doses >90 mg/m2 and affected up to 75% of 
patients treated with 200 mg/m2. The recommended phase II dose was 135 
mg/m2 administered over at least 1 hour every four weeks.  

23 
 
 
A review of several studies to evaluate overall safety in 682 patients who had 
received oxaliplatin either as a single agent or in combination with 5-FU was 
done to delineate the character and severity of oxaliplatin-induced 
neurotoxicity.46 Grade 3 neurotoxicty presenting as fine movement disturbance 
or moderate sensitive ataxia was observed in12% of patients at a median 
cumulative dose of 900 mg/m2 oxaliplatin. Total cumulative doses of 780, 1170, 
and 1560 mg/m2 were correlated with an incidence of 10%, 50%, and 75% 
neurotoxicity, respectively. The total cumulative dose of oxaliplatin was the most 
significant prognostic factor for the occurrence of neurotoxicity and inversely 
related to the likelihood of recovery from toxicity. Symptoms resulting from 
Grade 1 and 2 neuropathy regressed in 82% of patients within 4 to 6 months, 
and disappeared entirely in 41% of patients within 6 to 8 months. In summary, all 
studies reported to date support that the neurotoxicty resulting from oxaliplatin 
treatment was specific, cumulative, and, unlike cisplatin-induced neuropathy, 
reversible in most patients. 
 
2.1.6.2.1 Combination 5FU/Oxaliplatin: mFOLFOX6 
 
5-FU and oxaliplatin combinations have proven activity in many tumor types 
including GEC, colon, breast, and lung.47,48  The tolerability and safety of this 
combination is well established, and has been administered in various forms 
including FOLFOX4, FOLFOX6 and FOLFOX7.40  Modified FOLFOX 
(mFOLFOX6) treatment, which entails bolus 5FU/LV and continuous infusion 
5FU over 48 hours, along with 85mg/m2 of oxaliplatin every other week, has 
become a standard administration schedule of the two chemotherapies.10,40 
Neutropenia, diarrhea and peripheral sensory neuropathy are the most 
significant toxicities encountered.48 
 
2.1.6.3 Irinotecan 
 
Irinotecan (CPT-11, Camptothecan) prevents DNA from unwinding by inhibition 
of topoisomerase I. It is a semisynthetic analogue of the natural alkaloid 
camptothecin. Initially showing benefit in metastatic colorectal cancer, in 
particular, in combination with other chemotherapy agents, it has become a 
common drug used in various malignancies, including GEC, pancreatic cancer 
and other gastrointestinal malignancies.  Irinotecan is activated by hydrolysis to 
SN-38, an inhibitor of topoisomerase I. This is then inactivated by 
glucuronidation by uridine diphosphate glucoronosyltransferase 1A1 (UGT1A1). 
The inhibition of topoisomerase I by the active metabolite SN-38 eventually 
leads to inhibition of both DNA replication and transcription.49  
The most significant adverse effects of irinotecan are severe diarrhea and bone 
marrow suppression, particularly neutropenia. Patients homozygous for the *28 
allele of UGT1A1 have been reported to be more susceptible to irinotecan 
toxicities, including neutropenia.50,51   
 
2.1.6.3.1 Combination 5FU/Irinotecan:  FOLFIRI 
 
Administration of FOLFIRI consists of the same bolus/infusional 5-FU/LV 
backbone schedule as within mFOLFOX6, with the replacement of oxaliplatin  
with180 mg/m2 of irinotecan. Randomized trials in colorectal cancer showed 

24 
 
improvements in clinical efficacy based on overall response rates, time to tumor 
progression, and median overall survival when irinotecan has been added to 
either infusional (FOLFIRI)52 or bolus (IFL).53 There is an abundance of preclinical 
and clinical evidence that there is synergistic effect of 5FU in combination with 
irinotecan, despite developed resistance to 5FU monotherapy or combination with 
prior platinum in various tumor types, including GEC.54-56   
 
2.1.6.4 Docetaxel 
 
Docetaxel (Taxotere) is a clinically well-established anti-mitotic chemotherapy 
medication that interferes with cell division. It is used in various malignancies, 
including GEC. Docetaxel may be administered IV weekly (25mg/m2, every 
other week (50mg/mg2) or every three weeks (75mg/m2) with relatively equal 
efficacy in the palliative setting.57  
 
Docetaxel is of the chemotherapy drug class of taxanes, and is a semi-synthetic 
analogue of paclitaxel (Taxol), an extract from the bark of the rare Pacific yew 
tree Taxus brevifolia.58 Due to scarcity of paclitaxel, extensive research was 
carried out leading to the formulation of docetaxel – an esterified product of 10-
deacetyl baccatin III, which is extracted from the renewable and readily available 
European yew tree.  Docetaxel differs from paclitaxel at two positions in its 
chemical structure. It has a hydroxyl functional group on carbon 10, whereas 
paclitaxel has an acetate ester, and a tert-butyl carbamate ester exists on the 
phenylpropionate side chain instead of the benzyl amide in paclitaxel. The 
carbon 10 functional group change causes docetaxel to be more water soluble 
than paclitaxel.58  
 
A model based on electron crystallographic density and nuclear magnetic 
resonance deconvolution has been proposed to explain the binding of docetaxel 
to β-tubulin.59 In this T-shaped/butterfly model, a deep hydrophobic cleft exists 
near the surface of the β-tubulin where three potential hydrogen bonds and 
multiple hydrophobic contacts bind to docetaxel. The hydrophobic pocket walls 
contain helices H1, H6, H7 and a loop between H6 and H7 that form 
hydrophobic interactions with the 3’-benzamido phenyl, 3’-phenyl, and the 2-
benzoyl phenyl of docetaxel. 3’-phenyl also has contact with β-sheets B8 and 
B10. The C-8 methyl of docetaxel has Van der Waals interactions with two 
residues, Thr-276 and Gln-281 near the C-terminal end of β-tubulin. Docetaxel’s 
O-21 experiences electrostatic attraction to Thr-276 and the C-12 methyl has 
proximity with Leu-371 on the loop between B9 and B10. 
 
Docetaxel exhibits cytotoxic activity on GEC, and various other malignancies.60 
Docetaxel does not block disassembly of interphase microtubules and so does 
not prevent entry into the mitotic cycle, but does block mitosis by inhibiting 
mitotic spindle assembly.61 Resistance to other chemotherapies including 
paclitaxel, the topoisomerase inhibitors doxorubicin or irinotecan, or platinum 
drugs, does not necessarily indicate resistance to docetaxel.32,60 Microtubules 
formed in the presence of docetaxel are of a larger size than those formed in the 
presence of paclitaxel, which may result in improved cytotoxic efficacy.62 
Abundant formation of microtubules and the prevention to replicate caused by 
the presence of docetaxel leads to apoptosis of tumor cells and is the basis of 

25 
 
docetaxel use as a cancer treatment.  Common adverse effects include 
alopecia, peripheral neuropathy and cytopenias.  
 
2.1.6.4.1 Combination 5FU/Docetaxel: FOLTAX 
 
The combination of 5FU/LV and docetaxel has evidence of significant synergistic 
effects, and lack of cross resistance to prior chemotherapies, including 
monotherapy or combination with 5FU and platinum, irinotecan, and 
anthracyclines in GEC.62-65  
 
The regimen combining docetaxel and 5-FU/LV (DF or FOLTAX) is 
administered similar to the 5FU/LV bolus/continuous infusion backbones of 
mFOLFOX6 and FOLFIRI, with the replacement of oxaliplatin/irinotecan 
with docetaxel.66 A phase II comparison of docetaxel combined with 
continuous-infusion FU (DF) with ECF, using a 21-day infusion schedule of 
FU, in 90 patients with metastatic gastric cancer was conducted.65 
Response rates (36% to 38%), time to progression (5.3 to 5.5 months), 
and overall survival (9.5 to 9.7 months) were comparable for DF and ECF. 
The only GI toxicity that exceeded a rate of 10% was stomatitis (13%) for 
the DF regimen (compared with a rate of 2% with ECF). Although grade 3 
or 4 neutropenia was substantial for DF (42%), neutropenic fever was 
uncommon (4%). The results for DF compare favorably with DC or DCF 
and suggest that DF is a more tolerable alternative to DC or DCF, with 
lower rates of neutropenia and neutropenic fever.65 Moreover, consensus 
is that the use of weekly or biweekly infusion of FU is preferable given the 
superior toxicity profile.14,56,66 
 
The use of 5FU/LV bolus/infusion along with oxaliplatin and docetaxel (FLOT) 
administered IV biweekly has a favorable safety profile. FOLTAX is a modified 
FLOT regimen without the oxaliplatin, and a slightly different 5FU/LV 
administration which is identical to 5FU/LV administration within the mFOLFOX6 
and FOLFIRI regimens.67   
 
2.1.7 HER2 positive GEC 
 
2.1.7.1 HER2 Positivity in Advanced Gastric/EGJ Cancer 
 
Human epidermal growth factor receptor 2 (HER2) (ERBB2) positivity, defined 
as overexpression of the cell surface receptor or amplification of its encoding 
gene, has been reported in a number of solid tumors and has been shown to 
confer adverse clinical prognosis particularly in breast cancer.68-70  
 
In a literature survey of studies of HER2 overexpression in GEC tumors, 16 
studies reported HER2 positivity assessed by immunohistochemistry (IHC).71 In 
these studies, 3264 tumor specimens were tested, with a mean overall HER2 
positivity rate of 17.6% (range, 6.8%–34.0%), with a mean rate of 14.0% in 
studies from Asian institutions and a mean rate of 19.8% in studies from non-
Asian institutions. In another nine studies, HER2 positivity was assessed by in 
situ hybridization (ISH) methods. In 1232 tumor specimens, the mean overall 
HER2 positivity rate was 19.2% (range, 7.1%–42.6%), including mean rates of 
14.9% in studies from Asian institutions and 18.6% in studies from non-Asian 
institutions.71 The high variability in the HER2-positivity rates can be partly 

26 
 
explained by the fact that initial HER2 data were generated using the breast 
cancer HER2 testing or scoring principles (or both), or were performed with 
non-validated tests. 
 
As part of eligibility screening for a large randomized trial (Study BO18255, 
ToGA) that tested the safety and efficacy of adding anti-HER2 therapy to 
standard fluoropyrimidine/cisplatin chemotherapy for the treatment of advanced 
GEC, 3667 evaluable tumor samples (representing the largest cohort assessed 
in a central laboratory with the same assays and a standardized read-out) were 
tested by IHC and ISH methods, with HER2 positivity requiring either IHC 3+ 
(any FISH score) or ISH+ (any IHC score 0-3+) results. The overall rate of 
HER2 positivity in the screened population for the ToGA trial was 22.1% using 
both criteria.72 Using current clinical standards, only ~15% of those patients on 
the ToGA trial would be considered HER2 positive (ICH2+ and FISH+, IC3+ 
irrespective of FISH).  
 
2.1.7.2 Trastuzumab in the Treatment of Advanced GEC 
 
The antitumor effect of trastuzumab (Herceptin®) against HER2-positive human 
GC cell lines of Western or Asian origin was demonstrated in nonclinical 
studies.73,74 Synergistic antitumor effects of trastuzumab plus chemotherapy 
agents such as platinum-based drugs and fluoropyrimidines were also reported 
in nonclinical models of HER2-positive human GC lines.74-76  
 
Based on nonclinical results and the proven clinical benefit of adding 
trastuzumab therapy to combination chemotherapy in the treatment of HER2-
positive breast cancer in both the metastatic disease and adjuvant treatment 
settings, a randomized Phase III study was undertaken to investigate the 
efficacy and safety of adding trastuzumab to combination chemotherapy with a 
fluoropyrimidine (capecitabine or 5-FU) plus cisplatin (FP) for the treatment of 
HER2-positive AGC (Study BO18255, ToGA).72 The study enrolled 594 patients 
in 24 countries. Patients were randomized in a 1:1 ratio to receive either the FP 
regimen alone or in combination with trastuzumab (TFP). The primary endpoint 
was OS. Treatment was six 3-weekly cycles of FP chemotherapy for all 
patients, with capecitabine or 5-FU chosen by the investigator for each patient. 
Patients randomized to the TFP regimen received trastuzumab every 3 weeks 
(Q3W) concurrently with chemotherapy; trastuzumab was then continued as a 
single agent until disease progression was documented by the investigator. 
 
Results showed that treatment with TFP was superior to FP alone, with a 
median OS of 13.8 months for patients in the TFP arm compared with 11.1 
months for those in the FP arm in the intent-to-treat (ITT) population (hazard 
ratio [HR] = 0.74; 95% confidence interval [CI]: 0.60, 0.91). In a post-hoc 
analysis among patients whose tumors highly overexpressed HER2 (IHC 3+ 
(the majority of which were ISH+) and IHC 2+/ISH+ -- the clinical criteria now 
used currently to determine positivity), a reduction of 35% in the risk of death 
(HR= 0.65; 95% CI: 0.51, 0.83) was observed with a median OS of 16.0 months 
in the TFP arm compared with 11.8 months in the FP arm. The most common 
adverse events (AEs) (nausea, vomiting, neutropenia), Grade 3–4 AEs, and 
cardiac AEs occurred at similar or identical frequencies in both treatment 
groups.72 
 

27 
 
The results of Study BO18255 (ToGA) have led to worldwide regulatory 
approvals of the cisplatin/5FU/trastuzumab regimen, and this regimen is a 
standard treatment for metastatic HER2-positive adenocarcinoma of the 
stomach and EGJ in the first line setting. (NCCN Clinical Practice Guidelines in 
Oncology, Gastric Cancer 2012). Given the known inter-changeability of 
cisplatin and oxaliplatin in various regimens, FOLFOX-trastuzumab 
combination is considered to be within treatment standards.14,15 
 
2.2 
Molecular Heterogeneity of GEC: Inter-Patient 
 
Regrettably, there are a number of recent examples of failed clinical trials in 
GEC that assessed the addition of novel biologic agents to standard 
chemotherapy treatment regimens.2 Failure to improve patient outcomes was 
likely due to a ‘one-size-fits-all’ treatment approach, and not taking into account 
inter-patient tumor molecular heterogeneity (inter-PH) at diagnosis - in other 
words, using ‘targeted therapies for un-targeted patient populations’.  Notable 
examples include (but not limited to) the REAL-3 trial (panitumumab), for 
previously untreated advanced GEC using chemotherapy with/without an anti-
EGFR antibody.77  Others include the negative AVAGAST (bevacizumab)78 and 
EXPAND (cetuximab)79 trials in the metastatic setting.  Another example is the 
large GRANITE-1 study using everolimus (mTOR inhibitor) versus BSC in the 
second-line setting.80 On the other hand, better outcomes have ensued when 
clinical trials attempted to select patients based on prospective molecular 
profiling of the tumors, based on sound preclinical evidence of predictive 
markers enriching for those patients most likely to benefit from the targeted 
agent.81 This provides rationale to ‘match’ a targeted biologic agent with a 
molecular target that has undergone genomic activation (‘oncogenic driver’) via 
either an activating mutation, amplification, or translocation, or somewhat less 
so with proteomic aberration, namely protein overexpression. 
 
The recent ToGA trial, as above in Section 2.1.7.2, evaluated the addition of 
anti-HER2 therapy to standard chemotherapy, for stage IV GEC, which 
improved mOS, albeit modestly from 11.1 months to 13.8 months.72 In the 
subgroup of extremely high HER2 expression/gene amplification (defined as 
immunohistochemistry (IHC) 3+/ fluorescence in situ hybridization (FISH) 
positive) representing 44% of patients on trial, the mOS improvement was more 
pronounced, increasing from 12.3 to 17.9 months. This supports the notion that 
profiling tumors to identify a true oncogenic driver, and coupling this with specific 
therapeutic inhibition, will lead to better outcomes for patients.82  
 
Another encouraging example of improved outcomes based on tumor inter-PH 
profiling and patient selection for treatment is with anti-MET kinase treatment.  A 
recent phase II trial using anti-HGF antibody treatment (the growth factor for 
MET) improved mOS of stage IV GEC patients from 8.9 to 11.1 months for all 
(unselected) patients.83 However, in a retrospective analysis using an arbitrary 
cut-off of >50% MET expression (> 1+) by IHC in tumor cells as a predictive 
biomarker (~42% of patients on trial), it was observed that mOS was improved 
from 5.7 to 11.1 months in this sub-population. This confirmed MET high 
expression to be a poor prognostic marker and positive predictive marker to 
MET signaling pathway inhibition, as previously described. Importantly, those 
patients with low MET expression (~58% of patients) did slightly worse than in 

28 
 
the placebo arm, strengthening the argument and importance of patient 
selection for treatment. See section 2.5.1.2 for updated phase III results.  
 
In addition to HER284 and MET85,86, we and others have identified a number of 
other potential molecular oncogenic drivers contributing to inter-PH at relatively 
low frequencies within this disease87 with therapeutic potential, including RON88, 
FGFR289-91, EGFR92-94, HER395, IGF1R96,97, KRAS98,99, BRAF100, PIK3CA101,102 
and CCND1/CCNDE in human GEC samples and cell lines.103   A clearer 
understanding of the degree of inter-PH and the patterns of genomic profiles 
within GEC is desperately needed (Figure 4,5). An approach that acknowledges 
tumor heterogeneity between patients, in terms of best known oncogenic driver 
categories within GEC,7,87 is discussed in more detail below in Sections 2.4 and 
2.5. 
 
2.3 
Molecular Heterogeneity of GEC: Intra-Patient  
 
In addition to molecular heterogeneity between individuals (inter-PH) with GEC, 
there is an increasing recognition of molecular heterogeneity within any given 
individual (intra-PH) with GEC and other tumors (Figure 4,5).  This can be 
observed at any given time point (snap shot) of multiple locations of disease 
within the patient through space. Examples include: i) within the primary tumor, 
ii) from primary tumor to lymph node, iii) from primary tumor to metastatic 
lesion(s) and/or iv) from one metastatic lesion to another.  In addition to intra-PH 
through space, it is invariable that intra-PH occurs over time (particularly with 
treatment) as the tumor evolves and treatment selects for resistant clones. The 
nature of intra-PH, including through space and time, in GEC is not well 
characterized.5,104,105 
 
2.3.1 Molecular Heterogeneity Through Space 
 
Intra-PH through space, both within the primary site, and from primary site to 
metastatic disease locations has been described in several tumor types (Figure 
4,5,6). Discordance of a tumor molecular profile, due to intra-PH (from primary 
to metastatic lesion), was estimated to occur in colon cancer in up to 10-15% of 
cases.106,107 In our preliminary data, we have observed, in general, tumor 
evolution such that there is acquisition of additional genomic abberations (eg. 
MET, HER2, KRAS amplification in metastatic lesions not present in the primary 
tumor). Clearly, trials evaluating biologic agents that specify enrollment criteria 
based on primary tumor molecular profiles would therefore be susceptible to 
mis-classification, which may lead to confusing results, biasing towards the null 
if true positive patients are classified as negative for a given biomarker, 
explained further in Section 2.4.3 (Figure 5).  
 
2.3.2 Molecular Heterogeneity Through Time 
 
Ultimately, however, even considering examples of highly selected patients for 
therapy based on inter-PH (eg. HER2, MET), tumor resistance and progression 
occurs despite the ‘personalized’ therapeutic approach, a phenomenon that is 
eventually invariable (Figure 4,5B X-axis). This highlights the increasingly 
recognized phenomenon of intra-patient tumor heterogeneity (intra-PH) and 
tumor selection/evolution through time (ie. after treatment), which results in 
resistant clones.104,105,108     

29 
 
 
2.4 
Rationale of Mandatory Biopsies and Integral Biomarkers 
 
The promise of ‘personalized’ cancer care with therapies targeted toward 
specific molecular aberrations has great potential to improve clinical outcomes. 
However, there is emerging understanding of profound molecular heterogeneity 
within GEC (inter-PH), and within an individual (intra-PH) through space 
(primary tumor to metastasis) and time (resistance to treatment). This 
heterogeneity is a hurdle to advancing GEC treatment.1,2 Current clinical trial 
design paradigms are challenged by heterogeneity, as they are unable to test 
targeted therapeutics against low frequency genomic aberrations with adequate 
power.81,109  Accrual difficulties to GEC trials are exacerbated by low frequencies 
of molecular ‘oncogenic drivers’. Oncogenic drivers of GEC including MET 
amplification (not mere over-expression), FGFR2, and others, have even less 
frequent genomic activation (<10%) than HER2 (15-20%). The ToGA trial 
screened ~4000 patients in order to accrue adequate numbers for the primary 
endpoint. For biomarkers with lower incidence (<10%) this would require 
impossibly high screening numbers to attain adequate statistical power. 
Moreover, as we learn of more and more predictive biomarkers, there is limited 
tissue to test/screen for each of these using “à la carte” assays. To address this 
recognized challenge, there is need for novel clinical trial designs/strategies 
implementing medium throughput technologies in order to account for inter-
patient molecular diversity and tissue economy. Importantly, there is also need 
for predefined treatment algorithms given multiple aberrations observed within 
any one individual.1 Finally, access to multiple therapeutic agents are required to 
be available for treatment. Intra-PH may be addressed by post-treatment biopsy 
and repeating the ‘biomarker and treatment assignment algorithm’. This  
innovative clinical trial design, PANGEA (Personalized Anti-Neoplastics for 
Gastro-Esophageal Adenocarcinoma), integrates novel medium throughput 
proteomic and genomic technologies with a practical ‘biomarker assay and 
treatment algorithm’.2  Attempts to understand tumor evolution through time via 
less-invasive approaches will also be important, potentially by evaluating 
circulating tumors cells and/or circulating DNA (Figure 4).  
 
2.4.1 Rationale of Biopsies and Personalized Approach at Baseline 
 
Given the recognition of profound tumor molecular heterogeneity from one 
patient to the next, tissue screening within clinical trials use diagnostic biopsies 
for molecular profiling, in addition to establishing a diagnosis by standard 
pathological methods. The baseline diagnostic biopsy is usually performed on 
the primary tumor via upper endoscopy. However, on occasion given various 
scenarios, biopsy of metastatic lesions for diagnostic purposes is also 
performed. In our experience, there is often enough tissue remaining after 
diagnostic testing. However, it is not uncommon that repeat biopsy is required 
when little diagnostic tissue remains. In fact, in the standard clinical setting, up to 
25% of patients require repeat biopsy for HER2 testing that could not be 
performed on the original diagnostic sample.72 As discussed in section 2.6, in 
order to appreciate the individual’s tumor and the oncogenic drivers present 
within it, as well as molecular evolution from primary site to metastatic site, one 
must evaluate it.  
 

30 
 
However, mandatory biopsy of a metastatic lesion for patients with a known 
diagnosis poses its own challenges. The same is true for a proposed serial 
biopsy at each progression point.  On the other hand, prospective biopsy has 
been deemed safe in such a setting,110 and we believe that more accurate 
biomarker assignment (and treatment allocation) can be achieved by limiting 
false negative findings based on primary tissue, which in our experience may be 
as high as 10-15%.1,2,106,107 This clearly has the potential to benefit each patient 
individually, as the knowledge gained would apply directly to their treatment 
strategy at baseline, and over time with each subsequent line of therapy. 
Moreover, this strategy has great potential to enhance our understanding of both 
inter-PH and intra-PH via the proposed biopsy schedule (Figure 2,3,4,5). 
Recently, there is a trend for clinical trial biomarker screening to require ‘up-to-
date’ tumor biopsy to get the most relevant ‘snap-shot’ of the tumor biology. 
 
 
2.4.2 Addressing Inter-Patient Heterogeneity 
 
The understanding of inter-PH is one of extreme importance in the era of 
molecularly targeted therapies. Our understanding of redundant signaling as well 
as our success (limited) with inhibiting oncogenic drivers across tumor types 
including GEC (HER2+ and trastuzumab), brings the hypothesis of whether 
identifying an oncogenic driver at diagnosis and matching with a specific therapy 
that inhibits this driver directly will benefit patients.1,2,82 Molecular profiling at 
diagnosis attempts to stratify patients into ‘oncogenic driver’ categories (see 
Figure 1, 3, 6 and Section 2.5). Although, ultimately, each individual tumor 
profile is quite unique, we have determined that molecular patterns are prevalent 
and patients can be categorized into ‘dominant’ oncogenic driver categories as a 
compromise  – the hypothesis tested by PANGEA is whether this algorithm of 
categorization and consequent matched therapy, like with HER2+ tumors, will 
result in improved clinical outcome versus current standard cytotoxic therapy for 
HER2 negative tumors.  
 
2.4.3 Addressing Intra-Patient Heterogeneity Through Space 
 
In order to address whether the strategy delineated in section 2.5.1.6 is 
beneficial, we must be confident that patients are classified appropriately at the 
time of diagnosis/trial enrollment. We and others have demonstrated that 
patients’ tumors frequently experience molecular evolution from primary to 
metastatic lesion, including HER2 status (Figure 5). Given that most diagnostic 
biopsies are from the primary tumor, most molecular assays are performed on 
these tumors. However, approximately 10-20% of cases may evolve to acquire 
the presence of any given biomarker (e.g. HER2 or MET amplification, PI3K 
mutation etc.) that is only present in the metastatic lesion. In the instance of 
profiling only the primary lesion, a patient would be classified as negative for the 
biomarker, and therefore not assigned treatment with the appropriate therapy, 
thus biasing the results of the trial towards the null. Therefore, with biopsy of a 
dominant metastatic lesion (liver, lung, peritoneum, lymph node) as determined 
by the radiologist and treating oncologist, one will be able to assess both the 
primary and metastatic lesion. In the event of discrepancy, the molecular profile 
of the metastatic lesion will trump the primary tumor molecular profile, in terms of 
the final classification; it is important to note that there are few reports (if any) of 
LOSS of the status of the proposed biomarkers (HER2 amp+, MET amp+, 

31 
 
KRAS/PIK3CA, FGFR2 amp+, EGFR amp+) in metastatic lesions when present 
in the primary tumor. Therefore we are mostly attempting to detect those tumors 
in the metastatic space that have evolved to acquire the aberration during the 
passage from primary tumor location to metastatic site, although it is possible 
that some aberrations will be lost from primary to metastatic lesion. Importantly, 
assessment of multiple biomarkers will be done, such that although any one 
biomarker may not change status through space, this does not exclude the 
possibility that at least one concurrent aberration does. Therefore, estimated 
tumor evolution rates of 10-15% as determine by evaluating only 3 aberrations 
may actually be higher when looking at more biomarkers, supporting a biopsy of 
the distant site to adequately classify a patient’s tumor (Figure 3,5). 
 
 
 
 
2.4.4 Rationale of Serial Biopsy and Biologic Beyond Progression (BBP) 
2.4.4.1  Addressing Intra-Patient Heterogeneity Through Time with Serial 
Biopsies 
 
Despite accurate biomarker assessment and classification and optimal response 
to treatment, ultimately, tumors will evolve to demonstrate resistance to a given 
therapeutic regimen. We have shown that serial biopsies over time can identify 
resistance mechanisms that are either inherently present in a proportion of cells 
at the onset (original tumor biopsy) that are clonally selected by exposure to a 
particular therapy, or mechanisms that are up-regulated in cells as an acquired 
‘response’ in order to maintain viability, despite exposure to the treatment.98,111 
This has been demonstrated across tumor types, including GEC. Importantly, 
results from repeat biomarker assessment in these serial biopsies will allow for 
patients to cross over to alternate treatment categories if their disease evolves 
into that respective category, providing incentive and direct potential benefit to 
the patient undergoing the biopsy. An example is a patient with EGFR status 
(B8, Figure 3) who develops MET amplification after treatment with anti-EGFR 
agents as determined by post-treatment biopsy at PD1. This patient would be 
reclassified as MET+ (B2, Figure 3) in the treatment algorithm, and treated 
accordingly. 
 
2.4.4.2  Rationale of Continuation of Biologic Agents Beyond Progression (BBP) 
 
Significant evidence exists that maintenance of biologic ‘pressure’ on the 
presumed ‘driver’ with a BBP approach, improves clinical outcomes, including 
mOS (eg. BCR-ABL for CML, KIT mutation for GIST, HER2+ breast cancer, and 
anti-VEGF for colorectal cancer). Two strategies of BBP have been examined. 
The first is to declare the targeted inhibitor failed, but resume therapy with 
another inhibitor of the same target (eg. BCR/Abl-CML, KIT-GIST, HER2-
breast,GEC).112,119 On the other hand, continued inhibition of the target with the 
same molecular inhibitor but alteration of the cytotoxic chemotherapy backbone 
has also been successful (anti VEGF-A – Colorectal).113,114  Discontinuation of 
an active biologic agent (eg MET inhibitor for MET amplified tumor) at developed 
resistance (acquisition of KRAS amplification in addition to MET amplification) 
allows the tumor to revert back to its original MET amplification only status as 
the sole driver, suggesting that maintaining MET inhibition is required for best 
tumor control.107 Another advantage of BBP in the PANGEA trial is that it will 

32 
 
allow for a very accurate mOS since patients will be uniformly treated through 
three lines of therapy, which clearly does not occur in ‘one-line’ trials where 
patients’ treatment plans diverge significantly at second/third line therapy, and 
those enrolled in second or third line trials represent a selection bias not 
representing all patients with newly diagnosed GEC.  Therefore, PANGEA will be 
able to account for post-first (and second) line treatments, and compare to the 
historical control (in this pilot trial) or a randomized placebo control (in future 
planned randomized phase II trials). (Figure 1,2) 
 
 
 
2.5 
Biomarker Assessment and Treatment Algorithm 
 
  
2.5.1 Rationale of Molecular Categories and Treatment Assignment 
 
Molecular profiling of tumors has led to the observation that although ‘driver-
oncogene’ aberrations can be determined with novel medium-high throughput 
assays, the various genomic aberrations are not necessarily mutually exclusive 
(Table 1,2).1,2,115-118 One tumor sample may have up to 10 genomic aberrations. 
On average, we have observed ~3-5 genomic changes (mutations, 
amplifications, translocations) in GEC patients (Figure 6).1,2 Adding proteomic 
expression data to the genomic data adds another layer of complexity and ‘over-
lapping’ of potential treatment categories.119 Thus, in order to assign a patient to 
a predefined categorical molecular group that will be treated with one matched 
therapy, we have set a prioritization algorithm based on known clinical and 
preclinical information regarding the various potential molecular abnormalities 
(Figure 3). For instance, given the known benefit of HER2+ GEC with 
trastuzumab therapy, HER2+ status trumps all, and patients will be assigned to 
this group. (However, if other genes have higher amplification, they will take 
precedence). The next priority goes to MET amplification, which has strong 
preclinical evidence of therapeutic benefit from anti-MET agents, and also has 
positive randomized phase II data to support this. However, MET over-
expression is treated with less priority than EGFR and FGFR2 gene 
amplification, given each of these scenarios having strong preclinical evidence 
of ‘driver’ status. Therefore, MET overexpression (non-amplified) is lower than 
these groups. MSI-H/EBV/TMB>15mt/Mb/ PDL1+ CPS>10 patients, typically 
mutually exclusive to the Amplified patients will be next priority, with strong 
evidence to date with checkpoint inhibitors for these patients. Next would be the 
RAS/PI3K-like groups (having activation of either RAS/RAF/MEK and/or 
PI3K/mTOR/AKT and/or GNAS).  Because less overwhelming data exists for a 
matched agent for these groups, they take lower precedence, should a 
concurrent aberration be present (eg MET amp+, MET expression, etc.). Finally, 
for those ‘all-negative’ tumors, an anti-EGFR agent will be used here for those 
expressing EGFR by Mass Spectrometry (MS) (B8, Figure 3), and with VEGFR 
inhibition for MS negative (B9, Figure 3), with the rationale that other molecular 
groups that would be considered unlikely to respond to anti-EGFR (or anti-
VEGFR) have been removed, thus enhancing the possibility of benefit of the 
remaining patients to this therapy.  Assays used for biomarker assessment via 
the biomarker assessment and treatment algorithm are described in Section 
2.5.2. 
 

33 
 
*While we await drugs for arms other than those available, if a tumor is classified 
in a category where the drug is not yet available, they will proceed to the next 
priority level or treated as standard of care, per physician discretion, in this pilot 
study. 
  
 
2.5.1.1  HER2 
 
As discussed in 2.1.7, HER2 gene amplification and overexpression (HER2+) 
was evaluated in the ToGA trial where the addition of Trastuzumab to 
Fluoropyrimide/platinum resulted in improved OS in these HER2+ patients, 
becoming a new standard of care in the first line setting.72 Continuation of anti-
HER2 therapy after progression is currently unsupported and not recommended 
in GEC.  However, the TYTAN study recently showed that HER2+ patients do 
benefit in terms of mPFS and mOS in the second line therapy with lapatinib, 
after Trastuzumab failure, supporting the notion of continued pressure on HER2 
after first progression.120 Moreover, in HER2+ breast cancer, both lapatinib and 
TDM-1 have shown survival benefit with continuing HER2 inhibition after first 
progression with trastuzumab. This trial will test the continued use of 
trastuzumab while altering backbone chemotherapy in order to improve HER2+ 
patient outcomes over standard cytotoxic second/third line therapy alone.  
 
 
2.5.1.2  MET  
 
As discussed in section 2.2, another promising molecular subgroup of GEC are 
MET-driven tumors, either by MET gene amplification and consequent protein-
overexpression or by over-expression without gene amplification.83,86,121,122  A 
number of MET inhibitors are in development, including monoclonal antibodies 
to the ligand (eg. Rilotumumab, ficlatuzumab) as well as to the receptor itself (eg 
emibetuzumab, onartuzumab, ABT-700). Additionally, small molecule inhibitors, 
both classic ATP-competitive (Type I and II) as well as non-ATP-competitive 
inhibitor (ie. tivatinib), are in development.   
 
A phase II trial using anti-HGF antibody (rilotumumab) treatment (the growth 
factor for MET) improved mOS of stage IV GEC patients from 8.9 to 11.1 months 
for all (unselected) patients. However, in a retrospective analysis using an 
arbitrary cut-off of >50% MET expression (> 1+) by IHC in tumor cells as a 
predictive biomarker (~42% of patients on trial), it was observed that mOS was 
improved from 5.7 to 11.1 months in this sub-population.83 This confirmed MET 
high expression to be a poor prognostic marker and positive predictive marker to 
MET signaling pathway inhibition, as previously described. Importantly, those 
patients with low MET expression (~58% of patients) did worse than in the 
placebo arm, strengthening the argument and importance of patient selection for 
treatment.  
 
MET has been noted to be a resistance mechanism to a number of other 
targeted therapies. It is thus very possible that other treatment categories will 
‘migrate’ to the MET+ category at PD1 and/or PD2, thus potentially benefiting 
from anti-MET therapy at this time. 
 
Selection of MET positive tumors (defined as gene amplified or overexpressed 
by mass spectrometry) for treatment with a MET pathway inhibitor will comprise 
a molecular treatment category in the PANGEA trial (Figure 1,3). 

34 
 
 
Interim reports indicated that the phase III trial of ECX+/-rilotumumab would be 
halted for fultility (no safety issues) of reaching the primary endpoint,123 and we 
reported this recently at ASCO 2015. It should be noted that the selection of 
MET+ patients was via IHC testing, and ~80% of screened patients were 
deemed MET+ (likely to high). We propose in PANGEA that the cut-off of MET 
positivity should be much more stringent, based on our recent studies using 
mass spectrometry of approximately 25% positive rate.124 We will therefore use 
Mass Spectrometry (Oncoplex Dx) in a CLIA certified commercially available 
assay to determine treatment with MET antibody (TBD), not IHC, and believe 
that the potential benefit outweighs any potential risks. In fact, only <10% of 
patients actually had IHC2+ or greater and we believe that any true benefit in 
this subgroup would be concealed by the overwhelming majority of cases that 
were only 1+. Also, the recent onartuzumab phase II and III trials were reported 
both negative ITT. However, there were only 6 vs 8 patients in each arm with 
IHC 2+/3+ in the phase II, and therefore would be unable to detect even large 
benefit with such low numbers. Moreover, the phase III onartuzumab trial only 
had 40% of patients with IHC2+/3+ and in this subset of patients the HR for OS 
was 0.64 with p=0.06. The argument derived from both the rilotumumab and 
onartuzumab trials is that there was not sufficient power in the small subset of 
patients enrolled with truly high met expression in order to detect a HR of 0.5-
0.8, and that evaluating these patients specifically is still warranted and 
excluding those low-level expressors.  
 
     2.5.1.3  EGFR  
 
 EGFR is expressed in most GEC tumors at low/moderate levels. Gene 
amplification has been described in a much smaller subset of approximately 
5%.117,122 Numerous clinical trials have been conducted in GEC with various anti-
EGFR therapies, either alone or in combination, in unselected patient 
populations, including REAL3 (panitumumab),77 EXPAND (cetuximab),79 as well 
as trials with erlotinib.125,126 All of these trials reported unimpressive results.  In 
stark contrast to the HER2 (2.5.1.1) and MET (2.5.1.2) trials with their positive 
results, anti-EGFR therapy was not targeted towards tumors containing driver 
EGFR status (i.e. amplification, since EGFR mutation has not been described in 
GEC).  It is likely that anti-HER2 therapy would also have failed, or had only 
marginal benefit, if given to all GEC without selection, and similarly with anti-
MET therapy.  Moreover, recent analyses of both the REAL3 and EXPAND trials 
revealed that a subset of highly expressing EGFR tumors and/or those tumors 
possessing mutations that would predict lack of response (KRAS mutation etc.) 
derived OS survival benefit.77,127  
 
Given this background, PANGEA seeks to exclude tumors with known drivers 
that would be likely to render anti-EGFR therapy ineffective (HER2 amp+, MET 
amp+, FGFR2 amp+, KRAS amp+, PI3K mutation, etc.) and additionally select 
for those tumors that may actually be driven via the EGFR pathway from gene 
amplification. Preclinical models of cell lines with EGFR amplification are as 
sensitive to anti-EGFR therapy as HER2 amplified cell lines are to anti-HER2 
therapy, and anti-MET therapy for MET amplification.128   
 
2.5.1.4 
 FGFR2 
 

35 
 
FGFR2 is amplified in a subset of GEC of approximately 5-10%.129 Preclinical 
models with FGFR2 amplified GEC cell lines have demonstrated extreme 
sensitivity to FGFR inhibition, similar to the HER2, MET, and EGFR cases.129-133 
 
Antibodies and small molecules are in development targeting the FGFR2 
pathway in early phase clinical trials, many selecting for FGFR ‘activated’ status 
by either mutation or amplification in various tumor types.131 PANGEA includes 
FGFR2 as a molecular category within the trial.  
 
2.5.1.5 
MSI-H/EBV+/TMB>15mt/Mb/ PDL1+ CPS>10 
 
Microsatellite instability (MSI) can be assessed with routine clinical testing (using 
next generation sequencing NGS).  MSI-H tumors occur in approximately 5% of 
metastatic GEC. Reports now have established that these tumors may derive 
benefit from immune checkpoint inhibitors.  
 
EBV positivity (Ebstein Bar Virus, EBV+) can be assess by routine pathology 
EBER-ISH assay. EBV+ tumors occur in ~5% of metastatic GEC. Reports now 
have established that these tumors may derive benefit from immune checkpoint 
inhibitors. 
 
High Tumor Mutation Burden (TMB >15 mutations/Mb), usually occurs with MSI-
High tumors as above, but can sometime occur without MSI-High. These tumors 
have also had reported benefit from immune checkpoint inhibitors in other tumor 
types.  
 
PDL1+ CPS>10% can be assessed by routine IHC by the FDA approved 
companion diagnostic and can co-occur with any of the above (MSI-High, EBV+, 
TMB+) but can be present in the absent of these as well. These tumors have 
also had reported benefit from immune checkpoint inhibitors in this is other 
tumor types.  
 
Therefore, these groups are included and will be matched with anti-PD1 
antibodies along with standard chemotherapy in PANGEA.  
 
2.5.1.6 
KRAS/PIK3CA/AKT/GNAS (“KRAS-like”: VEGFR2) 
 
KRAS mutation is the most common oncogenic aberration in human 
malignancy.134 However, it is very rare in GEC amounting to 3% of cases.100 
However, we and others have reported that KRAS gene amplification (and less 
commonly NRAS mutation) can account for up to 10-15% of GEC cases, with 
consequent overexpression and dependence on the RAS/RAF/MEK pathway, 
and also co-dependence on the RAS-PI3K/mTOR/AKT pathway.87,99,135,136 
Moreover, PI3K mutation is frequently observed in up to 15% GEC patients, 
often in combination with HER2 amplification and KRAS amplification,137 with 
suggestion that this aberration renders resistance to anti-EGFR therapy similar 
to KRAS mutation for colon cancer.138  PTEN loss, BRAF mutation, and other 
aberrations in these signaling pathways including GNAS mutation, although 
relatively rare, and KRAS mutation, will also contribute to this group, which is 
herein referred to as “KRAS-like”.  
 

36 
 
In contrast to HER2, MET, EGFR, and FGFR2 receptor tyrosine kinase, the 
ability to directly inhibit KRAS has not been accomplished to date and the target 
has remained un-druggable to date likely due to inherent aspects of KRAS 
activation and affinity of GTP. Therefore, various indirect inhibition strategies 
have been or are being tested including farnesyl transferase inhibitors (inhibit 
cell surface association of KRAS), synthetic lethal partner inhibition, or inhibition 
of downstream effectors.  The first two approaches have resulted in 
unimpressive results, while the latter is the current approach undergoing active 
investigation.134  Another strategy of inhibition for KRAS driven GEC which has 
support preclinically and clinically is targeting blood vessel formation and 
angiogenesis.139-143  
 
The AVAGAST trial evaluated the anti-VEGF antibody, bevacizumab, with 
standard chemotherapy versus chemotherapy alone.78 Although mPFS was 
improved with statistical significance, mOS was not. Again, this trial was not 
designed to select any particular subset that may be more likely to derive 
benefit.  
 
Additionally, despite the negative results from AVAGAST, the REGARD trial was 
a global, randomized, double-blind, placebo-controlled trial of 355 (unselected) 
patients with disease progression on first-line platinum- or fluoropyrimidine-
containing combination therapy.144 It showed that the addition of ramucirumab, 
an anti-VEGFR2 antibody, to best supportive care significantly prolonged 
median overall survival—the primary endpoint—from 3.8 to 5.2 months (p = 
0.0473). This translated into a 22% reduction in the risk of death 
with ramucirumab. Ramucirumab monotherapy also prolonged median 
progression-free survival from 1.3 months to 2.1 months when added to best 
supportive care (hazard ratio: 0.483; p < 0.0001). Ramucirumab plus best 
supportive care more than doubled the disease control rate compared with best 
supportive care alone (48.7% vs 23.1%; p <0.0001).  
 
The randomized phase III clinical trials assessed combinations of ramucirumab 
with first- and second-line chemotherapy regimens in patients with advanced 
GEC. The results of the   phase III RAINBOW trial, evaluating second-line 
treatment with ramucirumab in combination with paclitaxel compared with 
paclitaxel alone, met its endpoint of improving overall survival: The OS hazard 
ratio (HR) was 0.807 (95% CI 0.678, 0.962; p=0.0169). Median OS was 9.63m 
for RAM+PTX and 7.36m for PTX. The HR for PFS was 0.635 (95% CI 0.536, 
0.752; p <0.0001). Median PFS was 4.40m versus 2.86m for the control arm. 
ORR was 28% RAM+PTX;16% PTX (p=0.0001).145 Moreover, if a subset of 
patients could be identified that responded with better outcomes, most patients 
could be spared from unnecessary treatments (cost and toxicity) while those 
who would be most likely to derive benefit would be treated. Therefore, 
treatment with anti-angiogenic agents is planned for the “KRAS-like” molecular 
category on PANGEA. 
 
In addition to the preclinical models discussed above regarding anti-
angiogenesis therapy in KRAS/PIK3CA driven cancer,143 it has been reported 
that the benefits of anti-VEGF therapy observed in colon cancer trials did not 
depend on KRAS or PI3K mutation status,140 suggesting that inhibiting the 
VEGFR pathway downstream from these genomic events was effective in these 
patients. Given the preclinical and clinical evidence that KRAS driven tumors 

37 
 
and PI3K driven tumors rely heavily on neo-angiogenesis, as well as the positive 
results from anti-VEGFR2 and/or anti-VEGF (mPFS) to date in GEC, a 
reasonable strategy would be to target this downstream effector for this 
molecular category.  PANGEA seeks to evaluate anti-angiogenesis in this study 
in this “KRAS-like” subgroup. 
 
2.5.1.7 
Rationale of Prioritized Treatment Algorithm 
 
 Above we have discussed a finite number of biomarker categories (HER2, MET, 
EGFR, KRAS/PI3K, FGFR2). This may be considered ‘futuristic’ in its approach 
to treating GEC particularly within one trial. Given the current strategy of defining 
HER2 positive versus negative, but otherwise treating all GEC patients similarly, 
the PANGEA design may be considered complicated and difficult to implement – 
this is the reason to commence with this pilot trial first for feasibility.  
 
However, it is becoming well-recognized that there are infinite possible 
molecular profiles (“n-of-one”), even within HER2 positive tumors (Table 1). An 
example of several GEC patients evaluated by NGS and FISH are demonstrated 
in Table 1. One can clearly observe the profound variability from one patient to 
the next in terms of molecular profiles. 
The 5-category biomarker classification as determined by the algorithm in 
Figures 3 and 6 is therefore largely a compromise from the true nature of inter-
patient heterogeneity. The 5 categories have been chosen based on their known 
preclinical and clinical evidence of ‘driver oncogene’ status and available 
therapeutic agents.2,87 It is very possible, and not uncommon, to have 
concurrent activation of one or more of the 5 categories as discussed above in 
section 2.5.1. Clear examples include HER2 amplification along with PI3K 
mutation and/or KRAS amplification.  Therefore, a prioritization of biomarker 
classification and treatment assignment (Figure 3) is required. This  
prioritization is proposed and follows logical reason, discussed in section 2.5.  
 
The highest priority is HER2 amplification and immunooncology (IO), given 
known clinical significance and the demonstrated evidence for anti-HER2 and 
anti-checkpoint therapy benefit for these patients.   
 
Next is the other receptor tyrosine kinase amplifications including MET 
amplification which has strong preclinical evidence of driver oncogene status 
and predictive value with respect to anti-MET therapy. Similarly, FGFR2 and 
EGFR gene amplifications, since these are similar to HER2 and MET as ‘driver’ 
aberrations. Although the 4 said genes are usually mutually exclusive, if in the 
event there is concurrent HER2, MET, FGFR2, and/or EGFR gene amplification 
in any combination, treatment category will be assigned by metatastatic samples 
(over primary samples) and prioritized treatment on the gene with the highest 
copy number. Example, if HER2 gene copy is 8 and EGFR is 70 (or ratio of 2 
versus 20+ for instance), treatment assignment will logically be EGFR. 
   
The next (sixth) category encompasses mutations and amplifications in the 
RAS/RAF/MEK/ERK and PI3K/PTEN/mTOR/AKT pathways (when the higher 
priority biomarkers are considered normal).  This “KRAS-like:VEGFR2” category 
will be assigned to anti-VEGFR2 therapy, as in Section 2.5.1.5. 
 

38 
 
Finally relegation cohorts #7 and #8 are if all other biomarkers are negative, 
where patients’ tumors having EGFR expression by Mass Spectrometry with be 
assigned to anti-EGFR therapy (ABT-806) and ‘all negative’ will be VEGFR2 
(ramucirumab). The rationale for EGFR as this ‘otherwise negative’ category (if 
expressing EGFR by MS) can be supported since we are excluding patients with 
other known driver oncogenes (HER2, MET, FGFR2, KRAS/PIK3CA, etc) that 
would predict against anti-EGFR therapy, enriching for a cohort that may gain 
benefit from targeting EGFR. If patients have QNS metastatic sample for full 
profiling and assignment, ctDNA NGS can be used, and if that is unrevealing, 
primary tumor can be used. If molecular profiling is overall QNS, then patients 
are assigned to #8 anti-VEGFR2.  
 
 
 
2.5.2  Background of Biomarker Assessment Techniques 
 
Bioassays and limited tissue (also see Section 9) 
 
Various techniques are available for tumor molecular characterization, each with 
its own sensitivity, specificity, advantages and disadvantages.146 Namely, high 
and medium ‘targeted’ throughput assays can quickly interrogate whole 
exomes/genomes for genomic aberrations or proteomic expression data in a 
timely manner, while two dimensional (2-D) histological data and tissue 
architecture is lost. Conversely, low-throughput assays do maintain tissue 
architecture, which is of extreme relevance when considering intra-PH within the 
tumor site, but is limited to one/few biomarker(s) and, in the case of FISH, is 
laborious, costly and time consuming.  Clinically for GEC, low-throughput 
techniques, including IHC and/or FISH have been approved for determination of 
protein overexpression and/or gene amplification, respectively, for HER2 
status.146,71,84 Similarly, IHC is currently the chosen method to select MET 
‘positive’ patients for clinical trial enrollment.83 Moreover, there is an increasing 
trend for clinical trials to specify enrollment criteria based on the availability of 
tissue for screening and selection for one target of interest (eg. HER2, MET, 
etc.).    
 
However, with increasing evidence of inter-PH as discussed above, and the 
scarcity of tissue from endoscopic or core needle diagnostic biopsies 
(particularly after standard clinical diagnostic tests are completed), there are 
significant limitations as to the number of low-throughput tests that can be 
performed on a given sample.146   With the introduction of several clinical trials 
operating in the same clinical indication, each requiring tissue for trial 
enrollment, an economical and pragmatic algorithm utilizing available bioassays 
and common molecular aberrations within GEC is desperately needed to best 
ration limited tissue samples and to best molecularly classify tumors for 
translational correlative research (Figure 4).  
 
Over the years, in order to facilitate high throughput testing of a limited tissue 
sample for gene expression, for both research purposes and clinical use, 
high/medium throughput gene expression assessments were accomplished by 
RNA extraction and either CHIP micro-arrays or RNA next-generation 
sequencing (NGS) assays.146 This was mostly due to the initial lack of 
availability of medium/high throughput proteomic assays. However, these RNA 
methods are highly dependent on tissue fixation, resulting in significant variation 
in reproducibility of results. In general, clinical tissues are formalin fixed and 

39 
 
paraffin embedded (FFPE) and by this process of fixation, time to fixation, along 
with storage time, the RNA becomes significantly degraded, subjecting these 
high-throughput assays to multiple deficiencies.146,147  Moreover, RNA 
expression, even in the best preserving circumstances, often does not correlate 
well with protein expression (as low as r2=0.3).88,148 However, selected reaction 
monitoring mass spectrometry (SRM-MS) has recently become available for 
targeted medium throughput assessment of protein expression in FFPE tissues, 
and therefore is no longer a limiting step.  We have shown using the ‘GEC-plex’ 
that FFPE tissues can be used for proteomic profiling that is not dependent on 
time to fixation or time from fixation or time from cutting the tissue block.119 This 
is in stark contrast to IHC and RNA-based tests, making this technology 
particularly attractive as a diagnostic clinical test.  
Given advances in technology available for molecular testing, there is increasing 
appreciation of tumor complexity and heterogeneity both between and within 
patients. There is also appreciation of the need to move away from a ‘one-size-
fits-all’ treatment strategy towards a more therapeutic approach premised on 
oncogenic ‘drivers’.82 There is significant uncertainty and controversy as to how 
to best accomplish the ‘personalized’ treatment of GEC.  Our preliminary data 
and the planned correlative studies within PANGEA-IMBBP aim to i) refine our 
understanding and evaluate the degree of inter-PH and intra-PH, through space 
and time using four (redundant) bioassays (proteomic: IHC, MS; genomic: FISH, 
NGS) in a panel of GEC cell lines and FFPE tumor tissues; ii) evaluate the 
correlation of results between each of these bioassays; and iii) further develop 
an algorithm to categorize patients into molecular subgroups that may better 
predict treatment benefit with currently available targeted agents.1,2   
2.5.2.1 
Fluorescence in Situ Hybridization (FISH) 
 
FISH testing is considered the gold-standard for gene copy number (GCN) 
testing within nuclei of interest.71 The test is low-throughput yet has many 
advantages over medium-high throughput assays that may also be able to 
determine GCN. Advantages include direct visualization of the probe within each 
individual nucleus, and therefore allows for counting of several nuclei (20-100, 
depending on study referenced) and ‘averaging’ of GCN/nucleus. Additionally, a 
control probe (CEP) for each gene is simultaneously hybridized in a different 
fluorescent wavelength, allowing for differentiation of increased GCN of the gene 
of interest (GOI) between amplification and mere polysomy (trisomy vs. low vs. 
high). A third probe for a second GOI on the same chromosome may be multi-
plexed (eg. tri-color FISH with MET/EGFR/CEP7 on chromosome 7). The ratio 
of the GOI/CEP is used to determine amplification status (>2 usually for GEC, 
such as for HER2 standard testing). Furthermore, maintenance of 2D tissue 
architecture allows for evaluation of tumor heterogeneity within the sample being 
assessed, as well as tumor GCN evolution from adjacent 
normalmetaplasiadysplasia carcinoma histological progression.  
 
FISH probes for each proposed GOI (HER2, MET, FGR2, KRAS, EGFR) have 
been characterized and evaluated extensively with reproducibility in the 
University of Chicago Clinical Cytogenetics Core Facility (CLIA).2,119 The HER2 
testing is performed per FDA guidelines (IHC and FISH). 
 

40 
 
However, disadvantages to this low-throughput technique are the cost, time, and 
use of 4uM of tissue per hybridization. Often, multiple 4uM slides are required 
per gene, in order to get an adequate tissue digestion and hybridization for 
reliable scoring. Additionally, this is operator dependent and scoring of nuclei 
can be subjective. This requires pathologist oversight to ensure proper nuclei 
are being scored. False results can be attained due to cross sectioning of nuclei 
whereby some signals would be lost. 
 
GCN by FISH has been shown to correlate well with protein expression by IHC 
for several genes, including HER2, MET, FGFR2, EGFR and KRAS in GEC and 
other tumor types. However, there is a discordance rate – for example several 
FISH+ patients in the ToGA trial were scored as IHC 1 or 0 occurring in 131/584 
= ~22% of patients enrolled.72 Importantly, the low expressing FISH+ patients 
derived no benefit from the addition of trastuzumab. 
 
Prospective evaluation of concordance of FISH status to IHC, MS, and NGS will 
be done, as well as correlation with clinical outcomes, both as univariate and 
multivariate (all genes of interest) analyses (see statistical methods section). 
 
Ultimately, for Gene Copy number and amplification should there be discrepancy 
between FISH and NGS, NGS will take precedence and be defined as >6 copies 
as in the Foundation One report.  
  
 
2.5.2.2 
Immunohistochemistry (IHC)   
 
 
IHC is a standard method to determine expression levels of a protein of 
interest.71,149  It is routinely used for HER2 evaluation in all GEC patients in the 
University of Chicago Department of Pathology (CLIA) per FDA guidelines. 
Similarly, MET, EGFR, KRAS, FGFR2, and PTEN have been validated for 
testing. Advantages of IHC are the relative ease, familiarity and expedient nature 
of the test. The 2D tissue architecture is maintained and therefore allows for 
assessing tumor heterogeneity, similar to FISH testing.  
 
On the other hand, each protein of interest tested requires 4uM of tissue, and 
given limited tissue availability, there is a finite number of tests that can be 
performed. Moreover, time to fixation, time from fixation, and time from cutting 
the FFPE tissue block can affect the accuracy of the results. Moreover, the 
primary antibody chosen to evaluate the expression may also affect results.  
 
Antibodies for the proteins of interest (HER2 – already clinical standard testing; 
and MET – MET4 antibody) have been validated and will be performed in the 
CLIA setting at Quintiles Westmont where already being performed in the 
RILOMET phase III trial. 
 
Prospective evaluation of concordance of IHC status to FISH, MS, and NGS will 
be done, as well as correlation with clinical outcomes, both as univariate and 
multivariate (all genes of interest) analyses.  
 
Ultimately, for protein expression of Met and Egfr, Mass Spectrometry will take 
precedence for assigning to the Met+ arm (#5 Figure 3) and the Egfr+ arm (#7 
Figure 3) using the Oncoplex Dx CLIA certified assay as in section 2.5.2.3. 
 

41 
 
2.5.2.3 
Mass Spectrometry (MS)  
 
Over the years, in order to facilitate high throughput testing of a limited tissue 
sample for gene expression, for both research purposes and clinical use, 
high/medium throughput gene expression analyses were accomplished by RNA 
extraction and either CHIP micro-arrays or RNA next-generation sequencing 
(NGS) assays.146 This was mostly due to the initial lack of availability of 
medium/high throughput proteomic assays. However, these RNA methods are 
highly dependent on tissue fixation, resulting in significant variation in 
reproducibility of results. In general, clinical tissues are formalin fixed and 
paraffin embedded (FFPE) and by this process of fixation, time to fixation, along 
with storage time, the RNA becomes significantly degraded, subjecting these 
high-throughput assays to multiple deficiencies.146,147  Moreover, RNA 
expression, even in the best preserving circumstances, often does not correlate 
well with protein expression (as low as r2=0.3).88,148 However, selected reaction 
monitoring mass spectrometry (SRM-MS) has recently become available for 
targeted medium throughput assessment of protein expression in FFPE tissues, 
and therefore is no longer a limiting step.  We have shown using the ‘GEC-plex’ 
that FFPE tissues can be used for proteomic profiling that is not dependent on 
time to fixation or time from fixation or time from cutting the tissue block.103,119,150 
This is in stark contrast to IHC and RNA-based tests, making this technology 
particularly attractive to develop as a diagnostic clinical test (Figure 4).  
 
Oncoplex Dx will perform exploratory MS analysis with CLIA/CAP certification, of 
all samples within PANGEA using the ‘GEC-plex’ assay, consisting of HER2, 
EGFR, MET, FGFR2, KRAS, and other peptides of interest including HER3, 
RON, SRC, IGF1R, FGFR1,PDL1, E-Cadherin, and Vimentin. 
 
Prospective evaluation of concordance of MS status to FISH, IHC, and NGS will 
be done, as well as correlation with clinical outcomes, both as univariate and 
multivariate (all genes of interest per laboratory correlatives Section 9) analyses. 
As in Figure 3, MS will take precedence when determining therapy in this 
pilot trial for the Egfr (#7) and Met expression arms (#5). 
 
 
 
2.5.2.4 
Next-Generation Sequencing (NGS) 
 
Our ability to amass large amounts of genetic information has far surpassed our 
experience and expertise regarding the clinical application of the derived 
material. Never has this discrepancy been more magnified - and have our 
limitations been so apparent - as with the advent of next-generation sequencing 
(NGS) (massive parallel end sequencing) technology and its role in modern-day 
oncologic practice.146,151,152   
 
Clinical Oncology is in the midst of a major paradigm shift.  Fueled by 
tremendous advances in molecular biology and technology, decisions regarding 
cancer care are increasingly being driven by data derived from NGS.  NGS will 
likely exponentially increase in the near future and may become universal as we 
strive for “personalized medicine.” 
 

42 
 
However, clinical trials, such as PANGEA, seek to evaluate the utility of NGS in 
routine clinical practice (Figures 4,6, Tables 1,2 in section 2.5.1.6). The 
profound inter-patient heterogeneity of tumor genomes and the large number of 
possible aberrations make this technology very powerful in order to quickly 
assess all potential relevant mutations, translocations, and/or gene copy 
changes with an economical amount of tissue using a ‘targeted’ oncology 
platform. This platform consists of known oncogenes and suppressors frequently 
(relatively) altered in cancers. Foundation One is a platform in routine use and 
will be performed for exploratory purposes on all samples within the trial. The 
methods are validated and the test is performed with CLIA certification.  
 
Prospective evaluation of concordance of NGS GCN and MSI status to FISH, 
IHC, and MS will be done, as well as correlation with clinical outcomes, both as 
univariate and multivariate (for genes of interest) analyses.  
 
Ultimately, for Gene Copy number and amplification should there be discrepancy 
between FISH and NGS, NGS will take precedence and be defined as >6 copies 
as in the Foundation  One report.  
 
 
2.5.2.1 
ctDNA NGS 
 
We will incorporate clinically available ctDNA NGS results at baseline and at 
progression to assist with treatment assignment, in particular when tissue 
biopsy of metastatic/progression site is not available/insufficient. 
 
2.6 
 Investigational Biologic Therapies 
 
2.6.1 Personalized Approach: Treating Oncogenic Drivers 
 
2.6.2 HER2: (Trastuzumab) 
 
Trastuzumab (lyophilized formulation) is available for commercial use as a 
freeze-dried preparation. All trastuzumab is supplied for IV administration. 
Trastuzumab is formulated in histidine, trehalose, and polysorbate 20. Vials of 
trastuzumab are shipped with cool packs at a temperature ranging from 
2°C−8°C (36°F−46°F) and must be placed in a refrigerator (same temperature 
range) immediately upon receipt to ensure optimal retention of physical and 
biochemical integrity. Temperature logs must be maintained (in accordance with 
local pharmacy practice) on the refrigerator to ensure proper storage conditions. 
Do not use beyond the expiry date stamped on the vial. DO NOT FREEZE. 
 
Trastuzumab may be sensitive to shear-induced stress (e.g., agitation or rapid 
expulsion from a syringe). DO NOT SHAKE. Vigorous handling of solutions of 
trastuzumab results in aggregation of the protein and may create cloudy 
solutions. Trastuzumab should be carefully handled during reconstitution. 
Causing excessive foaming during reconstitution or shaking the reconstituted 
trastuzumab may result in problems with the amount of trastuzumab that can be 
withdrawn from the vial. 
 
Dosage, Administration, and Schedule: See section 5.1.6. 
 
2.6.3 MET: (TBD) 

43 
 
 
 
.Dosage, Administration, and Schedule: See section 5.1.7. 
 
2.6.4 EGFR: (ABT806) 
 
The study drug and diluent must be refrigerated at 2°C to 8°C/36°F to 46°F, 
protected from light.  A storage temperature log will be maintained to document 
proper storage conditions.  The refrigerator temperature must be recorded on a 
daily basis on the temperature log to record proper function.  Temperature 
excursions must be reported to the Sponsor immediately.  The investigational 
products are for investigational use only and are to be used only within the 
context of this study.  The study drug supplied for this study must be maintained 
under adequate security and stored under the conditions specified on the label 
until dispensed for subject use or returned to the destruction facility. 
Study drug in vial form will be packaged in cartons.  Each vial and carton will be 
labeled per country requirements.  Labels must remain affixed to the vial and 
carton.  Refer to the detailed guideline:  Study Medication Preparation 
Guidelines, provided as a separate document outside of this protocol. 
 
Dosage, Administration, and Schedule: See section 5.1.8 
 
 
2.6.5 FGFR2 (TBD) 
 
 
Dosage, Administration, and Schedule: See section 5.1.9 
 
 
 
 
2.6.6  MSI-H/EBV+/TMB>15mt/Mb/ PDL1+ CPS>10 (nivolumab) 
 
Nivolumab is approved for various cancers. Although not approved for first line 
GEC, it is approved for MSI-H colon cancer tumors currently in the second line 
or higher, and also pembrolizumab another checkpoint inhibitor is approved for 
any tumor type with MSI-H including GEC. Pembrolizumab is now also approved 
for PDL1+ tumors in the third line setting or higher of GEC. Nivolumab is 
approved for GEC in the third line setting or higher in Japan. Therefore 
treatment with nivolumab will be conducted per package insert for MSI-High 
patients, as well as EBV+ and TMB>15mt/Mb and PDL1+ CPS>10 patients as 
these patients may also derive significant benefit from checkpoint inhibitors. 
 
 
 
 
2.6.7 KRAS/PIK3CA (Ramucirumab) 
 
Ramucirumab is now FDA approved for gastric, esophagogastric, and 
esophageal adenocarcinoma based on the REGARD153 and RAINBOW154 trials 
as monotherapy or combination with cytotoxic therapy, respectively. Therefore 
treatment with ramucirumab will be conducted per package insert.  
 
 
 
 

44 
 
 
3.     PATIENT SELECTION 
 
 
3.1   Eligibility Criteria  
     
 
 
 
 
 
 
1. Histologically confirmed metastatic gastric or esophagogastric junction (type 
I,II,III Siewert) adenocarcinoma  
 
2. Newly-diagnosed chemo-naïve or recurrent after curative-intent surgery 
 >6 months after completion of adjuvant therapy (including 
chemotherapy and/or radiotherapy) 
 No prior treatment with any targeted agent  
 Patients who have started first line mFOLFOX6 therapy (+/-
trastuzumab for HER2 amplified tumors) may be considered for trial 
participation if they have received no more than 4 doses of therapy at 
the time of consent and screening. 
1. These patients will be required to meet ‘next cycle’ parameters 
for eligibility before commencing treatment on trial (as per 
Section 6) rather than being required to meet parameters as 
indicated below in #12 which is for previously untreated 
metastatic/recurrent patients. 
 
3. Measurable metastatic disease by RECIST criteria,  
 Must be amenable to ultrasound or CT-guided biopsy of one 
metastatic lesion 
 Peritoneal disease as the sole site of occult metastasis or presenting 
as malignant ascites is acceptable if a cell block of tumor cells can be 
obtained showing >20% viable tumor cells. 
 
4. No currently active second malignancy 
 
5. No uncontrolled intercurrent illness or infection 
 
6. No peripheral edema > grade 2 at baseline. 
 
7. No peripheral neuropathy > grade 2 at baseline. 
 
8. No diarrhea > grade 2 at baseline. 
 
9. No autoimmune disease or chronic steroids (dose of >10 mg/day prednisone 
equivalent) or other immunosuppressive medications within 7 days of 
randomization (for MSI-H/EBV+/TMB-High>15mt-Mb/PDL1+ CPS>10% 
nivolumab group) 
 
10. ECOG PS 0-2 
 
11. Age > 18 years 
 
12. No CVA within 6 months, no recent MI within 6 months 
 
13. Patients must have normal organ and marrow function as defined below: 
 
 
 
- 
granulocytes 
 
>1,500/mcL 

45 
 
 
 
- 
platelets 
 
     >100,000/mcL 
 
 
- 
total bilirubin 
 
< 1.5 x ULN, <1.8 x ULN with liver metastases 
 
 
- 
AST(SGOT)/ALT(SGPT)           
 
 
 
 
<2.5 X ULN without liver metastases; 
 
 
 
 
 
 
 
 
<5 X ULN with liver metastases 
 
 
- 
creatinine within normal institutional limits (<1.5) 
 
 
 
 
 
 
 
 
 
 
OR 
 
 
 
- 
creatinine clearance   >50 mL/min/1.73m2,  
 
 
 
 
 (for creatinine level above normal) 
 
 
-       INR:   < 1.5 (patients on warfarin need to be converted  
 
 
        to LMWH during study participation to be eligible) 
       
                 
 
14. Consent to baseline metastatic and progressive disease biopsy (of 
metastatic/progressing lesion) for enabling biomarker assessment and 
treatment assignment (at each time point – baseline, PD1, PD2, PD3) as well 
as for correlative studies.  
 Consent to baseline and serial blood draws for plasma/serum/whole 
blood banking for correlative studies 
 
15.  Ability to understand and the willingness to sign a written informed consent 
document and consent to the serial nature of the proposed PANGEA  
treatment with first, second and third line therapy as tolerated. 
 
16.  Ability to comply with requirements of the protocol, as assessed by the 
investigator by the patient signing the consent form.  
 
17. If history of exposure to anthracyclines during perioperative treatment, the 
following cumulative doses of anthracyclines must be less than:  
Epirubicin  < 720 mg/m2  
Doxorubicin or liposomal doxorubicin < 360 mg/m2 
Mitoxantrone > 120 mg/m2 and idarubicin > 90 mg/m2  
  
If more than one anthracycline has been used, then the cumulative dose 
must not exceed the equivalent of 360 mg/m2 of doxorubicin.  
 
18. Cardiac Ejection Fraction >50% (for HER2+ patients) as assessed by 
echocardiogram, MUGA scan, or cardiac MRI  
 
19. Willingness to use effective and reliable methods of contraception (For 
appropriate methods of contraception considered acceptable see Appendix 
B). 
 
20. To commence second line irinotecan, bilirubin should be < 1 mg/dL. If 
between 1-2 mg/dL initial dose should be reduced by one dose level. If >2 
mg/dL, then irinotecan will not be used. 
 
21. To commence third line docetaxel, patients must have grade 2 or less 
neuropathy from prior oxaliplatin treatment. Also bilirubin > upper limit of 
normal (ULN), or AST and/or ALT > 1.5 x ULN concomitant with alkaline 
phosphatase > 2.5 x ULN are not eligible for docetaxel therapy. 
 

46 
 
22. Patients are allowed to consent to PANGEA as long as they have received 2 
months (4 doses) or less of FOLFOX (with or without 5FU/LV bolus) (plus 
trastuzumab if HER2 amplified) chemotherapy. 
 
3.2  Inclusion of Women and Minorities 
 
Both men and women and members of all races and ethnic groups are eligible 
for this trial.  
 
 
4. 
REGISTRATION PROCEDURES 
 
 
4.1 
General Guidelines 
 
All patients should be registered by the responsible Clinical Research 
Associate and/or Research Nurse in the eVelos Database prior the start of 
protocol-specific assessments.  All selection criteria listed in Section 3.0 
should be confirmed prior to registration. 
    
Following registration, patients should begin protocol treatment with FOLFOX 
chemotherapy and biologic agent (if assigned) within 14-days.  Issues that 
would cause treatment delays should be discussed with the Principal 
Investigator.   
 
**For HER2- subjects, they will receive standard chemotherapy alone.  If a 
targeted biologic becomes available for one or more of the other groups, the 
protocol will be amended to include new agents for the matched molecular 
group. Patients that started with chemotherapy alone will be candidates for 
adding the biologic agent when it becomes available along with whichever 
cytotoxic backbone regimen they are currently receiving, and will be considered 
having progression if CT shows progression after receiving 4 cycles of cytotoxic 
and backbone chemotherapy. IF PD on 4 cycles of cytotoxic chemotherapy prior 
to obtaining treatment assignment, patients can proceed to second line FOLFIRI 
and when assignment is learned added to FOLFIRI. However, if at C5 treatment 
assignement is known, patients may continue on FOLFOX first line therapy plus 
the newly assigned targeted therapy.  
 
Similarly, upon documented progression of disease by CT at first progression 
(PD1), ALL patients will undergo repeat biopsy and then change therapy to 
FOLFIRI cytotoxic and continue the biologic agent as assigned in the first line 
(Figure 2). Upon determination of biomarker classification and treatment 
assignment of the PD1 biopsy, patients may change to a new biologic therapy 
(with  FOLFIRI) if the molecular category changes from the originally assigned 
category. Similarly, at PD2, patients will change to FOLTAX chemotherapy and 
continue the biologic determined after PD1, and will switch biologic if the PD2 
biopsy assessment indicates to do so. The Principal Investigator will determine 
which biologic category will be assigned originally, and at PD1 and PD2, using 
the 4 diagnostic assays (FISH, IHC, MS, and NGS) as in section 2.5.2 and the 
biomarker assessment and treatment algorithm (Figure 3). Patients initially in 
one biomarker category that demonstrate tumor evolution into a different 
category, will change therapy to both the appropriate biologic therapy along with 
next cytotoxic therapy.  

47 
 
 
4.2 
Registration Process & Data Submission for Consortium Affiliates  
 
Not Applicable 
 
 
 
4.3 
Data and Safety Monitoring  
 
Data Safety and Monitoring will occur at the weekly University of Chicago GI 
Research Program meetings, which are led by senior level medical oncologists.  
At each meeting, the study will be reviewed for safety and progress toward 
completion. Toxicities and adverse events will be reviewed at each meeting.   
 
 
5. 
TREATMENT PLAN 
 
5.1 
Agent Administration and use of palliative therapy (ie Radiation) 
 
Treatment will be administered on an outpatient basis and follow the treatment 
strategy from first to second to third line (as tolerated) as depicted in the 
treatment schema and treatment strategy in Figures 1 and 2, respectively. A 
treatment cycle is defined as 2 weeks (14 days). Biologic agents will be 
assigned based on the biomarker category that the patient’s tumor is determined 
to be (Figure 3) at each time point (baseline, PD1, PD2). Appropriate dose 
modifications for each biologic agent and cytotoxic agent are described in 
Section 6.  Reported adverse events and potential risks for each biologic agent 
and each chemotherapy backbone (mFOLFOX6  FOLFIRI  FOLTAX) 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. In determining treatment doses for all agents, actual 
height and weight will be used for all calculations. Patient height and weight at 
screening will be used. This dose will be recalculated only if > 10% change 
in weight as per standard practice. There should be no adjustment to “ideal” 
weight. **In the event that scheduled intravenous treatment and/or clinic visits 
fall on holidays, the treatment may be given +/-3 days before or after these 
particular days. 
 
Palliative Radiation: Treatment interruption for palliative procedures such as 
radiation to painful lesions or bone metastases or an EGJ primary tumor causing 
dysphagia, as would be done standardly, is allowed, as long as systemic 
treatment is resumed within 6 weeks from last due dose. 
 
5.1.1 Safety Lead-In 
 
Because each chemotherapy regimen has not been previously combined, in 
some cases, with each proposed biologic agent, an initial group of 6 patients will 
receive open-label biologic agent within each treatment category (HER2+, 
MET+, etc.) for each cytotoxic backbone (mFOLFOX6, FOLFIRI, FOLTAX), with 
standard-doses of each cytotoxic, and each 6-patient cohort will be closely 
monitored.  
 
We conclude that a formal phase I study is not indicated for any of the 
investigational/cytotoxic combinations, since pre-clinical and clinical experience 

48 
 
with these proposed monoclonal antibody agents have shown that they do not 
substantially alter the toxicity profile of various chemotherapy regimens, 
including the cytotoxic agents included in PANGEA. This safety lead in will 
ensure that this is indeed the case prior to continuing with further enrollment.  
 
The initial 6 patients for any given treatment category and cytotoxic backbone 
will have completed 4 weeks of therapy with the combination and all data has 
been reviewed by the PI and drug sponsors (if applicable) prior to proceeding 
with the remaining portion of this study thereafter with respect to that biologic 
agent (treatment category) and cytotoxic backbone. Using the NCI CTC for 
adverse events v4.0, DLT will be defined as grade 4 thrombocytopenia, grade 4 
neutropenia lasting more than 7 days, grade 3 neutropenia complicated by fever 
or infection, or grade 3 or greater toxicity in other organ systems possibly, 
probably or definitely related to the biologic agent. If 1 DLT develops, 6 
additional patients will be accrued for a total of 12 patients. If 2 DLTs occur, 
accrual will be halted, and a dose de-escalation will be considered.  
 
If no investigator-determined DLTs have occurred in the first 6 patients on each 
combination or no more than 1 DLT in 12 patients on each combination, then the 
study can proceed to regular treatment within this particular category and 
cytotoxic regimen, once the Principal Investigator, has reviewed the data and 
concurs with the safety of this combination. 
 
5.1.2 Treatment Strategy: PANGEA 
 
Treatment will be administered on an outpatient basis and follow the treatment 
strategy from first to second to third line (as tolerated) as depicted in the 
treatment schema and treatment strategy in Figures 1 and 2, respectively. The 
biologic agents will be assigned based on the biomarker category the patient’s 
tumor is determined to be (Figure 3) at each time point (baseline, PD1, PD2).   
 
The pilot IMBBP with 4 of 6 molecular categories and biologic agents secured 
(IO: nivolumab; HER2++: trastuzumab;  EGFR++: ABT-806; VEGFR2++/+: 
Ramucirumab).   
 
The trial will be amended on a 'rolling basis' as the other drugs are secured for 
the other molecular arms. For patients’ tumors found to be in a molecular 
category without drug available at the time of enrollment (eg.FGFR2 amplified) 
they will be based on the prioritized treatment assignment in Figures 2 and 3). 
Accrual will be completed upon enrolling 68 patients within HER2++, MET++, 
EGFR++/+, VEGFR2++/+, and FGFR2++/MET++ if treated with anti-
FGFR2/MET antibodies] tumors, per the primary endpoint intention to treat (ITT) 
delineated in Section 13.  
 
Treatment assignment will be performed by the Principal Investigator, after 
reviewing all of the biomarker data for the patients’ tumors, at each timepoint 
(baseline primary/metastatic lesion, PD1, PD2) using the pre-specified treatment 
algorithm (Figure 3).  
 
 

49 
 
5.1.3    mFOLFOX6 
 
On day one of each treatment session patients will receive mFOLFOX6 with 
Oxaliplatin 85 mg/m2 given as a two-hour intravenous (IV) infusion. The dose of 
Leucovorin will remain fixed at 200 mg/m2 as a two-hour IV infusion followed by 
5-fluorouracil 400 mg/m2 IV push (bolus) and 5-fluorouracil 2400 mg/m2, given 
as a forty-six to forty-eight hour infusion (Continuous Infusion).  
 
 
 
 
mFOLFOX6 REGIMEN DESCRIPTION (FIRST LINE REGIMEN) 
 
Agent 
Dose 
Route 
Schedule 
Cycle Length 
Oxaliplatin 
85mg/m2 in 
500ml D5W 
IV over 2 hours 
before 5FU 
Day 1,  
week 1 
 
 
 
 
 
 
 
2 weeks  
(14 days) 
Leucovorin 
200mg/m2 in 
250ml D5W 
IV over 2 hours, 
can be given at 
the same time as 
Oxaliplatin in 
separate bags 
using a Y-line 
Day 1,  
week 1 
5-FU 
Bolus 
400mg/m2  
 
IV push 
Day 1,  
week 1 
5-FU 
2400mg/m2 
IV 
Via an 
ambulatory 
infusion pump of 
choice over 46-
48 hours 
Day 1,2 
 week 1 
Biologic 
Agent 
(as assigned) 
See respective 
5.1.(6-10) section 
depending on 
treatment 
category 
assignment 
IV 
(see dosing for 
each specified 
biologic agent in 
respective 
sections) 
Day 1,  
week 1 
 
 
 
Oxaliplatin may be given concurrently with Leucovorin 200 mg/m2. Oxaliplatin 
must not be mixed with normal saline; therefore, when Leucovorin and 
Oxaliplatin are given concurrently via a Y-connector, both drugs should be 
administered in D5W 
 
 
There is no clearly documented adverse impact of treatment of obese patients 
when dosing is performed according to actual body weight. Therefore, all 
dosing is to be determined solely by the patient’s BSA as calculated from 
actual weight. This will eliminate the risk of calculation error and the possible 
introduction of variability in dose administration. Failure to use actual body 
weight in the calculation of drug dosages will be considered a protocol 
deviation. Physicians who are uncomfortable with administering chemotherapy 
dose based on actual body weight should not enroll obese patients on this 
protocol. 
 

50 
 
 
Oxaliplatin is emetogenic. All patients receiving Oxaliplatin should be pre-
medicated with an acceptable antiemetic regimen. Patients may receive 
dexamethasone 10-20 mg IV as pre-treatment antiemetic unless there is a 
relative or absolute contraindication to corticosteroids. Other antiemetics may be 
used in addition to the suggested regimen, if clinically indicated. 
 
 
Hypersensitivity: Platinum hypersensitivity can cause dyspnea, bronchospasm, 
itching and hypoxia. Appropriate treatment includes supplemental oxygen, 
steroids, antihistamines, and epinephrine; bronchodilators and vasopressors 
may be required.  Platinum hypersensitivity is an extremely rare event and 
should be treated promptly. Oxaliplatin hypersensitivity occurs in approximately 
0.5% of patients receiving this agent. 
 
 
Pharyngo-laryngo dysesthesias: Oxaliplatin may cause discomfort in the larynx 
or pharynx associated with dyspnea, anxiety, swallowing difficulty and is 
exacerbated by cold. Appropriate therapy includes use of anxiolytics, cold 
avoidance and monitoring. 
 
 
Appropriate dose modifications for mFOLFOX6 are described in Section 6.   
 
 
Oxaliplatin may be held for up to 2 months for toxicity or other (i.e. break per 
OPTIMOX strategy), per physician discretion, and resumed by 2 months if: i) 
toxicity resolved to grade 1 or less, or if PD on maintenance 5FU. PD on 
mFOLFOX6 (PD1) is declared when: i) PD by RECIST 1.1 (section 11) after a 
two month round (4 cycles) of full cytotoxic backbone (mFOLFOX), ii) PD on 
5FU/LV alone and unable to resume Oxaliplatin due to toxicity > G1 (usually 
neuropathy) despite being off Oxaliplatin for 2 months, and ultimately iii) 
physician’s discretion.  
 
 
 
5.1.4    FOLFIRI (Second Line Chemotherapy Backbone) 
 
 
FOLFIRI REGIMEN DESCRIPTION (SECOND LINE REGIMEN) 
 
Agent 
Dose 
Route 
Schedule 
Cycle Length 
Irinotecan 
180mg/m2 in 
500ml D5W 
IV over 2 hours 
before 5FU 
Day 1,  
week 1 
 
 
 
 
 
 
 
2 weeks  
(14 days) 
Leucovorin 
200mg/m2 in 
250ml D5W 
IV over 2 hours, 
can be given at 
the same time as 
Oxaliplatin in 
separate bags 
using a Y-line 
Day 1,  
week 1 
5-FU 
Bolus 
400mg/m2  
 
IV push 
Day 1,  
week 1 
5-FU 
2400mg/m2 
IV 
Via an 
ambulatory 
infusion pump of 
choice over 46-
48 hours 
Day 1,2 
 week 1 
Biologic 
Agent 
See respective 
5.1.(6-10) section 
IV 
Day 1,  
week 1 

51 
 
(as assigned) 
depending on 
treatment 
category 
assignment 
(see dosing for 
each specified 
biologic agent in 
respective 
sections)
 
 FOLFIRI consists of 5-FU, Leucovorin, and Irinotecan. The dosing regimen 
for each subject will adhere to the protocol specifications. FOLFIRI dosing 
regimen will consist of l-LV 200 mg/m2 or dl-LV 400 mg/m2 as a 2-hour 
infusion, and Irinotecan 180 mg/m2 given as a 90-minute infusion in 500 mL 
dextrose 5% via a Y-connector, followed by bolus FU 400 mg/m2 and a 46-
hour infusion FU 2400 mg/m2. 
 
 Appropriate dose modifications for mFOLFIRI are described in Section 6. 
 
 Per treating physician discretion, testing for UGT1A1 genotype and dose 
reduction can be performed per clinical standards.   
 
 Doses of 5FU (bolus and continuous) within FOLFIRI should be continued 
from prior regimen dosing (ie mFOLFOX6), if dose reductions have occurred 
in the first line.  
 
 Irinotecan may be held for up to 2 months for toxicity or other (i.e. break per 
OPTIMOX/OPTIMIRI strategy), per physician discretion, and resumed by 2 
months if: i) toxicity resolved to grade 1 or less, or if PD on maintenance 
5FU. PD on FOLFIRI (PD2) is declared when:  i) PD by RECIST (section 
11) after a two month round (4 cycles) of full cytotoxic backbone (FOLFIRI), 
ii) PD on 5FU/LV alone and unable to resume Irinotecan due to toxicity > 
grade 1 despite being off Irinotecan for 2 months, and ultimately iii) 
physician’s discretion.  
 
5.1.5    FOLTAX (Third Line Chemotherapy Backbone) 
 
 
 
 
mFOLTAX REGIMEN DESCRIPTION (THIRD LINE REGIMEN) 
 
Agent 
Dose 
Route 
Schedule 
Cycle Length 
Docetaxel 
50mg/m2 in 
500ml D5W 
IV over 2 hours 
before 5FU 
Day 1, 
week 1 
2 weeks 
(14 days) 
Leucovorin 
200mg/m2 in 
250ml D5W 
IV over 2 hours, 
can be given at 
the same time as 
Oxaliplatin in 
separate bags 
using a Y-line 
Day 1, 
week 1 
5-FU 
Bolus 
400mg/m2 
IV push 
Day 1, 
week 1 

52 
 
5-FU 
2400mg/m2 
IV 
Via an 
ambulatory 
infusion pump of 
choice over 46-
48 hours 
Day 1,2 
week 1 
Biologic 
Agent 
(as assigned) 
See respective 
5.1.(6-10) section 
depending on 
treatment 
category 
assignment 
IV 
(see dosing for 
each specified 
biologic agent in 
respective 
sections) 
Day 1, 
week 1 
 
 FOLTAX consists of 5-FU, Leucovorin, and Docetaxel. The dosing regimen 
for each subject will adhere to the protocol specifications. FOLTAX dosing 
regimen will consist of l-LV 200 mg/m2 or dl-LV 400 mg/m2 as a 2-hour 
infusion, and docetaxel 180 mg/m2 given as a 90-minute infusion in 500 mL 
dextrose 5% via a Y-connector, followed by bolus FU 400 mg/m2 and a 46-
hour infusion FU 2400 mg/m2. 
 
 Appropriate dose modifications for mFOLTAX are described in Section 6.   
 
 Doses of 5FU (bolus and continuous) within FOLTAX should be continued 
from prior regimen dosing (i.e. mFOLFOX6, FOLFIRI), if dose reductions 
have occurred in the first line/second line.  
 
 Patients being considered for third line mFOLTAX are required to have 
grade 2 or less neuropathy from prior oxaliplatin treatment to be 
eligible.  
 
 Docetaxel may be held for up to 2 months for toxicity or other (i.e. break per 
OPTIMOX/OPTIMIRI/OPTITAX strategy), per physician discretion, and 
resumed by 2 months if: i) toxicity resolved to G1 or less, or if PD on 
maintenance 5FU. PD on FOLTAX (PD3) is declared when: i) PD by 
RECIST (section 11) after a two month round (4 cycles) of full cytotoxic 
backbone (FOLTAX), ii) PD on 5FU/LV alone and unable to resume 
Docetaxel due to toxicity > G1 (usually neuropathy) despite being off 
Docetaxel for 2 months, and ultimately iii) physician’s discretion.  
 
 
 
5.1.6 Trastuzumab (Herceptin) – HER2++ Patients 
 
 Trastuzumab will be administered intravenously on Day 1 of each treatment 
cycle, using an initial dose of 6 mg/kg for Cycle 1, followed by doses of 4 
mg/kg Q2W for subsequent treatment cycles. 
 
 Trastuzumab will be given until disease progression in the first line (PD1) 
(mFOLFOX6+trastuzumab) for HER2+ patients, or the development of 
unacceptable toxicity, or the patient is withdrawn from study treatment for 
another reason. 
 

53 
 
 The initial dose of Trastuzumab (Cycle 1, Day 1) will be administered over 90 
(± 10) minutes, after the patient will be observed for infusion associated 
reactions (IARs) such as fever, chills, headache, pruritus, nausea or 
vomiting, changes in vital signs, etc. If such symptoms occur, slowing or 
interruption of the infusion may be helpful, and the infusion can be resumed 
when symptoms abate. If the initial infusion is well tolerated, subsequent 
infusions may be administered over 30 (± 10) minutes, followed by an 
observation period of 30 minutes. 
 
 Patients who experience infusion-associated symptoms may be 
premedicated for subsequent infusions using acetaminophen/paracetamol 
and antihistamines. Dose reduction of Trastuzumab for toxicity is not 
permitted. Dose delays are permitted for toxicity, including cardiotoxicity 
documented by a symptomatic or an asymptomatic decrease in LVEF (see 
Section 6). See section 6 for cardiac imaging specifications (at least every 3 
months while on Trastuzumab). 
 
 If the patient misses a dose of Trastuzumab for any cycle (i.e., the two 
sequential administration times are 4 weeks or more apart), a reloading dose 
of 6 mg/kg of Trastuzumab should be given. If reloading is required for a 
given cycle, the study therapies should be given at the same schedule. 
Subsequent maintenance Trastuzumab doses of 4 mg/kg will then be given 
Q2W, starting 2 weeks later. 
 
 HER2+ patients will continue with Trastuzumab therapy after PD1 and PD2 
with the other cytotoxic backbones, FOLFIRI and FOLTAX, respectively, 
unless HER2+ status changes to one of the other 4 categories at PD1 or 
PD2 biopsy and molecular assessment. If molecular classification changes at 
either of these two time points, biologic treatment will change to the new 
appropriate drug for that molecular category. Trastuzumab will continue with 
second/third line cytotoxic regimen until biomarker assessment results are 
available from the PD1/PD2 biopsy.  
 
 
 
 
 
5.1.7 MET++ Patients (TBD)  
 
 
 
 
Patients may be able to receive anti-MET antibodies on other studies, 
and if so, they will be followed for survival outcomes and other translational correlatives as 
per the PANGEA study, but treated according to protocol of the other specific study with 
the anti-MET antibodies. At disease progression, they could then proceed with PANGEA 
protocol for subsequent lines of therapy per PANGEA protocol. These patients will be 
considered towards intention-to-treat population if indeed they receive the appropriate 
antibodies at each line of therapy along with chemotherapy, otherwise they will be included 
in a secondary exploratory analysis.  
 
 
 
 
5.1.8 (ABT806): EGFR++/+ patients 
 
ABT-806 24 mg/kg will be given every other week by IV infusion preceded 
approximately 30 minutes prior with 650 mg acetaminophen and 25 to 50 mg IV 
diphenhydramine.  Administration rate should not exceed 15 mg/min or be 
completed earlier than 15 minutes.   
 

54 
 
Subjects will be closely monitored for treatment-related adverse events, 
especially allergic reactions, during the infusion and the post-infusion 
observation hour.  For the initial ABT-806 infusion, pre-infusion vital signs should 
be taken. Direct observation is required for the first 15 minutes of the infusion 
and subjects should be closely monitored during the post-infusion hour.  For 
subsequent infusions, direct observation is not required; however, pre-infusion 
vital signs should still be taken. 
 
Severe allergic reactions (Grade 3 or 4) require the immediate interruption of 
ABT-806 treatment and permanent discontinuation from further treatment.  
Moderate allergic reactions (Grade 1 or 2) will also require the immediate 
interruption of ABT-806 treatment.  Once symptoms have resolved, retreatment 
is allowed with a 50% reduction of the infusion rate. 
Guidelines for dose, dose preparation, volume, rate of infusion and type of 
infusion pump device will be supplied by Abbott.  Acetaminophen and 
diphenhydramine will be supplied by the site.   
 
 
 
5.1.9 (TBD): FGFR2++ patients 
 
Patients may be able to receive anti-FGFR2 antibodies on other studies, and if so, 
they will be followed for survival outcomes and other translational correlatives as per the 
PANGEA study, but treated according to protocol of the other specific study with the anti-
FGFR2 antibodies. For example, the Phase I FIGHT study is a study assessing the new 
combination of FPA144 plus FOLFOX chemotherapy. For this phase I open label study, 
this FOLFOX-FPA144 combination allows for any line of therapy. So should a patient 
require anti-FGFR2 therapy at any line of therapy during enrollment on PANGEA due to 
FGFR2 amplification, then the patient could enroll in the FIGHT study to gain access to the 
FGFR2 inhibitor, as long as FOLFOX therapy could be considered appropriate for them. At 
disease progression, they could then proceed with PANGEA protocol for subsequent lines 
of therapy per PANGEA protocol. These patients will be considered towards intention-to-
treat population if indeed they receive the appropriate antibodies at each line of therapy 
along with chemotherapy, otherwise they will be included in a secondary exploratory 
analysis.  
 
 
 
5.1.10 (Nivolumab) MSI-H/EBV+/TMB-High>15mt-Mb/PDL1+ CPS>10% 
 Nivolumab will be administered intravenously on Day 1 of each treatment 
cycle, using an initial dose of 3 mg/kg for each Cycle Q2W 
 Treatment will be administered per FDA approved package insert 
 
 
 
5.1.11 (Ramucirumab): VEGFR2++/+ patients 
 Ramucirumab will be administered intravenously on Day 1 of each treatment 
cycle, using an initial dose of 8 mg/kg for each Cycle Q2W. 
 Treatment will be administered per FDA approved package insert 
 
5.2 
 General Concomitant Medication and Supportive Care Guidelines 
 
 
5.2.1 Antiemetics: Antiemetic medication may be used prior to treatments at 
the treating physician’s discretion.  
 
5.2.2 Growth Factors: Colony-stimulating factors (i.e., G-CSF) may be used if 
required. CSFs should be used according to ASCO guidelines. 
  
5.2.3 Central Access Device: is required for 5FU continuous infusion.  

55 
 
 
 
5.3  Duration of Therapy on Trial  
 
In the absence of treatment delays due to adverse events, treatment on trial 
(mFOLFOX6FOLFIRIFOLTAX, each with appropriate biologic therapy) may 
continue until one of the following criteria applies:  
 
 Disease progression as defined by PD3 or after 4 years on trial, whichever 
occurs first.  
 
 Intercurrent illness that prevents further administration of treatment,  
 
 Unacceptable adverse events(s),  
 
 Patient decides to withdraw from the study, or  
 
 General or specific changes in the patient's condition render the patient 
unacceptable for further treatment in the judgment of the investigator.  
 
 Patients who are discontinued from 1 or more agents for reasons of toxicity 
may continue on the remaining agents until one of the criteria above is 
reached.  
 
 Death 
 
5.4  Duration of Follow Up  
 
All patients will be followed until disease progression (PD1, PD2, PD3), and for 
any therapies received (what they are, and their duration) after PD3, and for 
survival until death or at 5 years from enrollment.  
 
6. 
DOSING DELAYS/DOSE MODIFICATIONS 
 
Dose Modification 
 
Chemotherapy dosing will be based on the patient’s baseline weight 
measurement. Weight will be measured on Day 1 of each 2-week treatment 
cycle. If there is a ≥10% change from the patient’s baseline weight 
measurement, the chemotherapy dose should be recalculated using the new 
weight. 
 
To the extent possible, the causal relationship(s) for each AE should be 
considered independently for each component of study treatment, and dose 
modifications (dose delays or dose reductions) should be applied only for the 
component(s) of study treatment that are causally related to a given AE.  
 
For non-hematologic toxicities that are likely a combination of both cytotoxic 
agents, removal of the 5FU bolus/LV will be the first dose modification, 
without altering the other cytotoxic (5FU continuous infusion, oxaliplatin, 
irinotecan, or docetaxel).  Subsequent recurrences of a similar toxicity will 
result in dose reduction of both cytotoxics (5FU continuous infusion and one 

56 
 
of oxaliplatin, irinotecan, docetaxel) as in Tables 3-7 below, or per the 
discretion of the treating physician.  
 
 
 
 
 
6.1  5-FU/Leucovorin – Non-Hematologic 
 
Re-treatment should be delayed until all non-hematologic toxicities have 
subsided to Grade ≤ 1. Treatment may be delayed up to 4 weeks (i.e., 6 weeks 
since the start of the previous treatment cycle) to allow for this recovery. If the 
patient cannot meet the re-treatment criteria at this time point, 5-FU should be 
permanently discontinued because of unacceptable toxicity. 
 
*First, omit the bolus 5FU and LV for any grade 2 or higher Hematologic or 
Non-Hematologic toxicity that may be attributable to 5FU either alone or in 
combination of other cytotoxics. Treatment should be held until resolution 
to Grade 1 or less, and then resume without the 5FU bolus.  
 
Then, based on the most severe toxicity experienced since the previous 
treatment, the following dose modifications should be used for non-hematologic 
toxicities. Table 3 provides further 5FU dose reductions for the first appearance 
(after dropping 5FU/LV bolus) of the specified toxicities.  
 
At each subsequent appearance of the toxicities, despite a prior dose reduction, 
the 5-FU dose could be further adjusted, if the treating physician considers the 
reduction to be in the best interest of the patient (otherwise the treatment should 
be discontinued). (eg. The second dose adjustment is by 25% of the previous 
dose (consistent with dose changes in Table 3)).   
 
Table 3: 5-FU Dose Modifications for Non-Hematologic Toxicities  
(if recurrent after dropping bolus) 
     
        Toxicity 
Grade 
5-FU 
 
 
First drop bolus for any toxicity, then: 
Nausea or vomiting, or both 
3 or 4 
75% of previous dose 
Diarrhea 
3 or 4 
75% of previous dose 
Stomatitis 
3 
75% of previous dose 
Stomatitis 
4 
50% of previous dose 
Cardiac toxicity (vasospasm) 
(attributed to 5-FU) 
 
2 
 
Stop 5-FU permanently 
Skin toxicities (HFS) 
3 or 4
75% of previous dose
Fatigue 
3 or 4
75% of previous dose
 
 
Nausea and Vomiting 
For Grade 3 or 4 nausea or vomiting, or both, the patient must have recovered to 
Grade ≤1 before treatment can be re-initiated. 
 
 
Diarrhea 
Doses should be reduced according to Table 3. After Grade 3 or 4 diarrhea, the 
patient must have recovered to Grade ≤ 1 before treatment can be re-initiated. 
 

57 
 
 
Stomatitis 
After Grade 3 or 4 stomatitis, the patient must have recovered to Grade ≤ 1 before 
treatment can be re-initiated.  
 
 
Skin Toxicity (Hand-Foot-Syndrome) 
Treatment will be withheld for Grade 3 or 4 toxicity until recovery to Grade ≤1. 
 
Fatigue 
 
Treatment will be withheld for Grade 3 or 4 toxicity until recover to Grade ≤1. 
 
 
Other Toxicities 
Other toxicities not listed above should be managed symptomatically, if possible, if 
they are Grade ≤2. For Grade 3 AEs, chemotherapy should be withheld for a 
maximum of 4 weeks beyond the scheduled treatment date (6 weeks since the start 
of the previous treatment cycle) until toxicity is resolved to Grade ≤1, then continued 
at a lower dose, if medically appropriate. After recovery from Grade 3 to Grade ≤1, 
a dose reduction of 25% of the previous dose should be made for subsequent 
cycles. If there is no resolution to Grade ≤1 after a maximum of 4 weeks beyond the 
scheduled treatment date of the next cycle (6 weeks since last dose), the patient 
should be permanently discontinued from 5-FU treatment. In case of Grade 4 
severity of toxicities other than those specified above, the patient will have 5-FU 
treatment held and the AE will be followed up until resolution of toxicity according to 
the protocol (grade 1 or less) and then resume at the appropriate at 75% of the 
previous dose, or not resume at all, ultimately per physician discretion. 
 
NOTE: There are no dose reductions for leucovorin. The dose remains fixed at 
200 mg/m2. Leucovorin is discontinued only when 5-FU bolus is discontinued.400 
mg/m2 racemate (d,l-leucovorin) may be a replacement in shortage of l-leucovorin.  
 
Thromboembolism 
Subjects who experience any grade ≥ 3 venous thromboembolic event while on 
study treatment may be treated with full dose anti-coagulation therapy with low 
molecular weight heparin (LWMH) (preferred) or other standard anti-coagulation if 
unable to receive LWMH. 
 
6.2 
Oxaliplatin 
First, omit the bolus 5FU and LV for any Hematologic or Non-Hematologic 
toxicity that may be attributable to 5FU either alone or in combination of other 
cytotoxics.  If the patient requires further oxaliplatin dose reductions than listed in 
the protocol (Tables 4-7), the patient will be removed from treatment with that 
agent. If the patient is removed from treatment with 5-FU or 5-FU treatment is held, 
oxaliplatin should be discontinued or held until 5-FU is resumed. If unable to 
resume 5FU, proceed to next line of therapy (irinotecan) alone without 5FU.  
 
      6.3    Irinotecan  
To commence second line irinotecan, bilirubin should be < 1 mg/dL. If between 
1-2 mg/dL initial dose should be reduced by one dose level. If >2 mg/dL, then 
irinotecan will not be used.  First, omit the bolus 5FU and LV for any 
Hematologic or Non-Hematologic toxicity that may be attributable to 5FU either 
alone or in combination of other cytotoxics. If the patient requires further 
irinotecan dose reductions than listed in the protocol (Tables 4-7), the patient will be 
removed from treatment with that agent. 

58 
 
     
  6.4    Docetaxel  
To commence third line docetaxel, patients must have grade 2 or less 
neuropathy from prior oxaliplatin treatment. Also bilirubin > upper limit of 
normal (ULN), or AST and/or ALT > 1.5 x ULN concomitant with alkaline 
phosphatase > 2.5 x ULN are not eligible for docetaxel therapy. First, omit the 
bolus 5FU and LV for any Hematologic or Non-Hematologic toxicity that may 
be attributable to 5FU either alone or in combination of other cytotoxics.  
If the patient requires further docetaxel dose reductions than listed in the protocol 
(Tables 4-7), the patient will be removed from treatment with that agent. 
 
Table 4: Dose Adjustment Levels for Any Toxicities for Cytotoxics (Oxaliplatin, 
Irinotecan, and Docetaxel).  
 
First Line 
Oxaliplatin 
 
Second Line 
Irinotecan 
Third Line 
Docetaxel 
 
Starting Dose 
 
 
85mg/m2 
 
 
180mg/m2 
 
50mg/mg2 
 
Dose -1 
 
 
65mg/m2 
 
135mg/m2 
 
37.5mg/m2 
 
Dose -2 
 
 
50mg/m2 
 
100mg/m2 
 
25mg/m2 
If the patient requires further dose reductions than listed in the protocol in the table 
above, the patient will be removed from treatment with that agent. If the patient is 
removed from treatment with 5-FU or 5-FU treatment is held, oxaliplatin should be 
discontinued or held until 5-FU is resumed. Single agent irinotecan or docetaxel is 
permitted. 
 
Table 5: Hematologic Dose Reductions (to be followed after 5FU bolus and LV 
dropped for first attributable toxicity occurrence as in Section 6.1). 
Toxicity 
Action 
Dose Modification 
 
Neutropenia1 
 
 
Grade 1 (ANC>1.5 x 10
9/L)  
 
 
Continue Treatment 
 
Maintain Dose Level 
 
Grade 2 (ANC 1.0 x 10
9/L – 
1.5 x 10
9/L) 
 
 
Continue Treatment 
 
Maintain Dose Level 
 
Grade 3 (ANC 0.5 x 10
9/L – 
1.0 x 10
9/L) 
 
 
Hold Treatment 
 
Recheck blood counts weekly 
until ANC > 1 x 10
9/L, then 
restart treatment.  
 
 
 
Decrease Cytotoxic one 
dose level. 1  
If the patient is not receiving 
cytotoxic, decrease 
continuous 5FU 75% from 
prior dose.  

59 
 
 
Grade 4 (ANC<0.5 x 10
9/L) 
 
 
Hold Treatment 
 
Recheck blood counts weekly 
until ANC > 1 x 10
9/L, then 
restart treatment.  
 
 
First Occurrence:  
Reduce Cytotoxic one dose 
level. 1 
 
Second Occurrence:  
Decrease 5-FU 75% from 
prior dose and cytotoxic one 
dose level. 1 
 
 
Neutropenic Fever1 
 
 
Grade 3 (ANC 0.5 < 1.0 x 
10
9/L) AND fever >38.5°C  
 
 
Treat neutropenic fever 
according to standard 
guidelines.  
 
Proceed with next cycle when 
fever is resolved and  
ANC > 1.25 x 10
9/L. 
 
 
First Occurrence:  
Reduce Cytotoxic one dose 
level. 1 
 
Second Occurrence:  
Decrease 5-FU 75% from 
prior dose and cytotoxic one 
dose level. 1 
 
 
Grade 4 (ANC 0.5 < 1.0 x 
10
9/L) AND fever >38.5°C  
Life-threatening 
consequences including 
septic shock, hypotension, 
acidosis 
 
 
Treat neutropenic fever 
according to standard 
guidelines.  
 
Proceed with next cycle when 
fever is resolved and  
ANC > 1.25 x 10
9/L. 
 
First Occurrence:  
Reduce Cytotoxic one dose 
level. 1 
 
Second Occurrence:  
Decrease 5-FU 75% from 
prior dose and cytotoxic one 
dose level. 1 
 
Thrombocytopenia 
 
 
Grade 1 (PLT >75 0 x 10
9/L) 
 
 
Continue Treatment 
 
Maintain Dose Level 
 
Grade 2 (PLT 50 x 10
9/L - 75 x 
10
9/L) 
 
 
Continue Treatment 
 
Maintain Dose Level 
 
Grade 3 (PLT 50 x 10
9/L - 75 x 
10
9/L) 
 
 
Hold treatment.  
Recheck blood counts weekly 
until PLT > 75 x 10
9/L, then 
restart treatment.  
 
 
Reduce Cytotoxic one dose 
level.  
If the patient is not receiving 
cytotoxic, decrease 
continuous 5FU 75% from 
prior dose. 
 
Grade 4 (PLT < 25 x 10
9/L) 
 
 
Hold treatment.  
 
Reduce Cytotoxic one dose 
level.  
If the patient is not receiving 
cytotoxic, decrease 

60 
 
Recheck blood counts weekly 
until PLT > 75 x 10
9/L, then 
restart treatment.  
 
continuous 5FU 75% from 
prior dose. 
ANC = absolute neutrophil count; PTL = platelet count   
1 At the investigator’s discretion growth factors may be used according to standard practice 
guidelines. 
 
Table 6: Non-Hematologic (except Neurotoxicity) Dose Reductions (to be followed 
after 5FU bolus and LV dropped for first attributable toxicity occurrence as in 
Section 6.1). 
 
Toxicity 
Action 
Dose Modification 
 
Grade 1 
 
 
Start Medical management. 
Continue Treatment 
 
 
Maintain Dose Level 
 
Grade 2 
 
Start Medical management. 
Continue treatment. 
 
If grade 2 toxicity (eg. 
diarrhea) persists despite 
aggressive medical 
management, may drop 
continuous 5FU and partner 
cytotoxic one dose level at 
physician discretion. 
 
 
Grade 3 
 
Start Medical management. 
Hold all treatment until 
resolved to Grade ≤1 
 
 
Decrease 5FU (per Table 3) 
and partner cytotoxic one 
dose level.  
 
Grade 4 
 
Start Medical management 
Hold all treatment until 
resolved to Grade ≤1 
 
Decrease 5FU (per Table 3) 
and partner cytotoxic one 
dose level. 
 
Table 7: Dose Modifications for Oxaliplatin or Docetaxel3 Induced Neurotoxicity 
 
Toxicity 
 
Duration of Toxicity 
 
 
Persistent 
Toxicity 
(at next due 
cycle) 
 
1-7 Days 
 
 
>7 Days & <14 
Days 
 
 
Grade 1 
Paresthesias/dysesthesias
1of 
short duration that resolves and 
do not interfere with function 
 
No Change 
 
No Change 
 
No Change 
 
Grade 2  
Paresthesias/dysesthesias
1  
interfering with function, but not 
activities of daily living (ADL). 
 
No Change 
 
No Change 
 
Decrease 
cytotoxic by one 
dose level. 

61 
 
 
 
Grade 3  
Paresthesias/dysesthesias
1  
with pain or with functional 
impairment that also interfere with 
ADL.  
 
1
stevent: 
Decrease 
cytotoxic by 1 
dose level.  
2 
ndevent: 
Decrease 
cytotoxic by a 
second dose 
level. 
 
 
Discontinue 
cytotoxic 
 
Discontinue 
cytotoxic 
 
Grade 4  
Paresthesias/dysesthesias
1  
that are disabling or life-
threatening. 
 
 
Discontinue 
cytotoxic 
 
Discontinue 
cytotoxic  
 
Discontinue 
cytotoxic 
 
Pharyngo-laryngeal 
dysesthesias (All Grades) 
 
 
Increase duration 
of infusion to 6 
hours
2. 
 
 
Increase duration 
of infusion to 6 
hours
2. 
 
Increase duration 
of infusion to 6 
hours
2 
1May be cold-induced.  
2Infusions extended to 6 hours because of toxicity may be administered over 2 days. 
Treatment continuation or discontinuation ultimately up to treating physician. 
 
3 To commence third line docetaxel, patients must have grade 2 or less neuropathy 
from prior oxaliplatin treatment. Treating physician may start docetaxel at one dose 
level lower for grade 2 oxaliplatin-induced neuropathy, at his/her discretion. 
 
 
6.5    Trastuzumab  
 
Trastuzumab administration may be delayed to assess or treat AEs, such as cardiac 
events. However, no dose reduction is permitted for Trastuzumab. 
 
If Trastuzumab is held for more than two cycles or needs to be permanently discontinued, 
the patient will be continued with cytotoxic treatment (and other biologics if appropriate), 
and the patient will continue to be followed after treatment as described in Section 5. 
 
Dose Delays or Discontinuations due to Cardiac Events 
In this study, all patients must have a baseline LVEF value ≥ 50%, and LVEF is to be 
monitored at least every 12 weeks during Trastuzumab antibody treatment. To ensure 
patient safety, if an investigator assesses that an AE may be related to cardiac dysfunction, 
an additional LVEF measurement should be performed, as well as other appropriate 
procedures such as chest X-ray, and the scheduled cardiac toxicity assessments will 
continue unchanged. 
 
If symptomatic LVSD (CHF) is confirmed by a cardiologist’s evaluation in any patient, 
Trastuzumab should be permanently discontinued, and the patient will continue cytotoxic 
chemotherapy (and other biologic therapy as appropriate) as tolerated, and followed per 

62 
 
protocol. Symptomatic LVSD should be treated and monitored according to standard 
medical practice. 
 
At the present time, there are inadequate data available to assess the prognostic 
significance of clinically asymptomatic decreases in LVEF values. However, if a patient’s 
LVEF value decreases to < 50% and with an LVEF decrease of ≥ 10 points from 
baseline in the absence of symptoms, treatment with Trastuzumab should be 
withheld temporarily and the LVEF measurement repeated in 4 weeks. If decreased 
LVEF is confirmed, Trastuzumab should be permanently discontinued and the patient may 
be treated with cytotoxic therapy as tolerated, per protocol (see figure below).  
 
LVEF, the algorithm shown in the Figure below should be followed to assess the LVEF 
decrease and determine whether to stop or continue study treatment (with both antibodies 
and chemotherapy, if the patient is still receiving chemotherapy). 
 
Infusion-Associated Reactions 
Administration of Trastuzumab may result in infusion-associated symptoms such as 
nausea, pyrexia, diarrhea, chills, fatigue, and headache, or allergic reactions. The 
majority of hypersensitivity reactions was mild or moderate in severity and resolved 
upon treatment. 
 
Study treatment will be administered in a clinical treatment setting with emergency 
equipment and staff who are trained to monitor for and respond to medical 
emergencies. Any patient who experiences a Grade 4 allergic reaction, bronchospasm, 
or acute respiratory distress syndrome (ARDS) associated with Trastuzumab will not be 
rechallenged with Trastuzumab.  
 
Patients who experience infusion-associated symptoms may be managed by slowing or 
interrupting the Trastuzumab infusion and by providing supportive care with oxygen and 
medications (e.g., beta-agonists, antihistamines, antipyretics, corticosteroids), as 
determined by the investigator to be clinically appropriate. 
 

63 
 
In patients who have experienced infusion-associated symptoms, premedication with 
antipyretics, antihistamines, or corticosteroids may be used before subsequent 
infusions of Trastuzumab. 
 
Any patient who experiences infusion-associated symptoms should be monitored under 
clinical observation until complete resolution of all signs and symptoms of the infusion-
associated reaction. 
 
On very rare occasions, patients have experienced the onset of infusion symptoms or 
pulmonary symptoms more than 6 hours after the start of the Trastuzumab infusion.  
Patients should be warned of the possibility of such a late onset and should be 
instructed to contact their physician if these symptoms occur. 
 
If a patient cannot tolerate Trastuzumab infusions, Trastuzumab treatment will be 
permanently discontinued, but chemotherapy backbone may continue. 
 
Incomplete Dose Administration 
If a patient receives an incomplete dose of Trastuzumab because of an infusion related 
reaction or another reason, the following guidelines should apply: The patient should 
receive at least 50% of the dose during the first week of the treatment cycle. 
 
Therefore, if the patient receives < 50% of the dose, the patient should receive the 
remainder before Day 15 preferably within the first week. Thereafter, the patient should 
receive the usual maintenance dose 2 weeks after the first interrupted dose as routinely 
scheduled. 
 
• 
If the patient has received 50%–75% of the dose during the first week of the 
treatment cycle, the remainder should be given during the same treatment cycle 
(i.e., before Day 15 of that cycle), preferably before the end of the first week (i.e., 
before Day 8). 
 
• 
If the patient received > 75% of the dose, the remainder should be given during the 
same treatment cycle (i.e., before Day 15 of that cycle). Alternatively, the patient 
may be given a reloading dose on Day 1 of the following treatment cycle. 
 
• 
Please refer to Section 5.1.6 for guidance on re-loading in the event of missed 
Trastuzumab dose. 
     
6.6     FGFR2 antibody (TBD)   
    
 
6.7 ABT-806 
 
If at the start of a cycle (ie, day 1 of a cycle) cytotoxic chemotherapy is held due to 
toxicity, then ABT-806 treatment will be held until the subject has recovered (in 
accordance with protocol guidelines). If ABT-806 is held due to toxicities, but 
cytotoxic chemotherapy has not met criteria for withholding per protocol, then 
cytotoxic chemotherapy may be administered. A missed dose of ABT-806 will not 
be made up. 
 
If a subject experiences a grade 3 or 4 adverse event (thought secondary to ABT-
806 such as edema), ABT-806  administration will be postponed until the toxicity 
resolves to grade 1 or returns to the subject’s baseline value with the exception that 

64 
 
ABT-806  may resume with grade 2 neutropenia (absolute neutrophil count (ANC) ≥ 
1 x109/L). 
 
Grade 1 and 2 infusion reaction: If a ABT-806 infusion is interrupted because of a 
grade 1 or 2 infusion reaction, the infusion may be restarted but at a reduced rate 
(50% rate reduction) after resolution of the event and stabilization of the subject 
(total infusion time increased up to 120 ± 10 minutes). All subsequent infusions 
should be administered at the reduced rate. If a subject is unable to complete an 
ABT-806 infusion on the day of the infusion due to an infusion reaction, then the 
remainder of the infusion will not be made up on subsequent days. For subjects 
who have had a grade 1 or grade 2 ABT-806 infusion reaction (that did not result in 
interruption of ABT-806 infusion) decreasing the ABT-806 infusion rate is at the 
discretion of the investigator. 
 
Grade 3 infusion reaction: Subjects, who experience a grade 3 infusion reaction 
during ABT-806 administration, will have the ABT-806 infusion stopped and the 
remainder of that ABT-806 infusion will not be administered. Continuation of 
subsequent ABT-806 dosing after a grade 3 infusion reaction will be based on the 
severity and resolution of the event, and the grade 3 infusion reaction must be 
reviewed by the PI to determine if the subject can resume ABT-806. If a decision is 
made to continue ABT-806 treatment, all subsequent infusions should decrease the 
ABT-806 infusion rate by 50% (eg, increase the ABT-806 infusion duration from 60 
± 10 to 120 ± 10 minutes).  
 
Grade 4 infusion reaction: Any subject who experiences a grade 4 infusion 
reaction must permanently discontinue ABT-806. 
 
If ABT-806 is discontinued, but chemotherapy has not met withdrawal criteria 
per protocol, then cytotoxic chemotherapy may be continued. 
 
 
6.8 Ramucirumab – dose adjustments and delays will be conducted per package insert. 
 
If ramucirumab is discontinued, but chemotherapy has not met withdrawal 
criteria per protocol, then cytotoxic chemotherapy may be continued. 
 
6.9 Nivolumab - – dose adjustments and delays will be conducted per package insert. 
 
If nivolumab is discontinued, but chemotherapy has not met withdrawal 
criteria per protocol, then cytotoxic chemotherapy may be continued 
 
6.10 MET Ab (TBD) 
 
7.  
ADVERSE EVENTS:  Definitions AND REPORTING REQUIREMENTS 
 
Adverse event (AE) monitoring and reporting is a routine part of every clinical trial. 
The characteristics of an observed AE (Section 7.2) will determine whether the 
event requires expedited reporting in addition to routine reporting. 
 
7.1  
Adverse Event Characteristics 
 
 CTCAE term (AE description) and grade:  The descriptions and grading 

65 
 
scales found in the revised NCI Common Terminology Criteria for Adverse 
Events (CTCAE) version 4.0 will be utilized for AE reporting.  All appropriate 
treatment areas should have access to a copy of the CTCAE version 4.0.  A 
copy of the CTCAE version 4.0 can be downloaded from the CTEP web site 
http://ctep.cancer.gov/protocolDevelopment/electronic_applications/ctc.htm. 
 
 Attribution of the AE: 
- 
Definite (5) – The AE is clearly related to the study treatment. 
- 
Probable (4) – The AE is likely related to the study treatment. 
- 
Possible (3) – The AE may be related to the study treatment. 
- 
Unlikely (2) – The AE is doubtfully related to the study treatment. 
- 
Unrelated (1) – The AE is clearly NOT related to the study treatment.  
 
7.2.  Adverse Event Definitions 
 
7.2.1    Adverse Event 
An adverse event is defined as any untoward medical occurrence in a clinical trial 
subject. The event does not necessarily have a causal relationship with study 
treatment. The investigator is responsible for ensuring that any adverse events 
observed by the investigator or reported by the subject are recorded in the subject’s 
medical record. The definition of adverse events includes worsening of a pre-
existing medical condition. Worsening indicates the pre-existing medical condition 
(eg, diabetes, migraine headaches, gout) has increased in severity, frequency, 
and/or duration, and/or has an association with a significantly worse outcome. A 
pre-existing condition that has not worsened during the study, and involves an 
intervention such as elective cosmetic surgery or a medical procedure while on 
study is not considered an adverse event. 
 
Disease progression itself is not considered an adverse event; however, signs and 
symptoms of disease progression may be recorded as adverse events or serious 
adverse events. Deaths due to progressive disease during treatment or 30 days 
after the protocol specified therapy is stopped, whichever is later, should be 
recorded as due to the primary tumor. If a new primary malignancy appears, it will 
be considered an adverse event. 
 
The treating physician is responsible for reviewing laboratory test results and 
determining whether an abnormal value in an individual study subject represents a 
change from values before the study. In general, abnormal laboratory findings 
without clinical significance (based on the treating investigator's judgment) should 
not be recorded as adverse events; however, laboratory value changes requiring 
therapy or adjustment in prior therapy are considered adverse events. Where 
applicable, clinical sequelae (not the laboratory abnormality) should be recorded as 
the adverse event. 
A persistent AE is one that extends continuously, without resolution, between 
patient evaluation time points. Such events should only be recorded once on the 
Adverse Event eCRF. The initial severity of the event should be recorded, and the 
severity should be updated to reflect the most extreme severity any time the event 
worsens. If the event becomes serious, the Adverse Event eCRF should be 
updated to reflect this. 
 
A recurrent AE is one that resolves between patient evaluation time points and 
subsequently recurs. 

66 
 
 
The treating investigator’s clinical judgment will be used to determine whether a 
subject should be removed from treatment or from the study due to an adverse 
event. A subject, or subject’s parent/legal guardian, may also voluntarily withdraw 
from treatment due to an adverse event. If the subject withdraws full consent, the 
subject should be encouraged to undergo, at a minimum, an end-of-study 
assessment. 
 
 
 
 
7.2.2 Serious Adverse Events 
 
An adverse event is considered serious if it results in ANY of the following 
outcomes:  
 
1) Death 
2) Life-threatening (e.g. places subject at immediate risk of death, this does not 
include events that might have caused death if they occurred a greater 
severity) 
3) 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.  
 
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 subject and may require medical or 
surgical intervention to prevent one of the outcomes listed in this definition.  
Examples of such events could include allergic bronchospasm, convulsions, and 
blood dyscrasias, DILI or events that necessitate an emergency room visit, 
outpatient surgery, or other events that require other urgent intervention. 
 
Since the criteria for CTCAE v4.0 severity differs from the regulatory criteria for 
serious adverse events, if adverse events correspond to grade 4 “life threatening” 
CTCAE v4.0 severity criteria (eg, laboratory abnormality reported as grade 4 
without manifestation of life threatening status), it will be left to the investigator’s 
judgment to also report these abnormalities as serious adverse events. For any 
adverse event that applies to this situation, comprehensive documentation of the 
event’s severity status must be recorded in the subject’s medical record. 
 
7.2.3  Unexpected Events 
 
Unexpected events are those not listed at the observed specificity or severity in the 
protocol (section 6), informed consent, investigator brochure, or FDA-approved 
package insert.  An event is considered unexpected if it is listed as occurring within 
the class of drugs or otherwise expected from the drug’s pharmacological properties 
but which has not been previously observed with this specific investigational agent. 
 
7.2.4  Adverse Reactions  
 

67 
 
An adverse event is considered to be an adverse reaction if there evidence to 
suggest a causal relationship to the study agent.  This may include a single 
occurrence of an event strongly associated with drug exposure (e.g. Stevens-
Johnson Syndrome), one or more occurrence of an event otherwise uncommon is 
the study population, or an aggregate analysis of specific events occurring at 
greater than expected frequency. 
 
7.3  
Reporting Procedures for Serious Adverse Events 
 
7.3.1  Routine Adverse Event Reporting 
 
All Adverse Events must be reported in routine study data submissions.  AEs 
reported using the Serious Adverse Event Reporting Form and/or MedWatch 
Form discussed below must also be reported in routine study data 
submissions. 
 
The principal investigator is responsible for ensuring that all adverse events 
observed by the investigator or reported by the subject that occur on or after the 
first treatment of study therapy through 30 (+ 3) days after the last administration of 
protocol specified therapy are reported using the applicable eCRF (eg, Adverse 
Event Summary eCRF). 
 
The investigator must assign the following adverse event attributes: 
 Adverse event diagnosis or syndrome(s), if known (if not known, signs or 
symptoms),  
 Dates of onset and resolution, 
 Severity (and/or toxicity per protocol), 
 Assessment of relatedness to biologic (ie trastuzumab or rilotumumab) 
and/or cytotoxic backbone (mFOLFOX6, FOLFIRI, FOLTAX) 
 Action taken. 
 
The adverse event severity grading scale used will be the CTCAE v4.0.  
 
The treating investigator (in communication with the PI) must assess whether the 
adverse event is possibly related to the investigational biologic product in question 
(eg. Trastuzumab or rilotumumab) and/or cytotoxic chemotherapy (mFOLFOX6, 
FOLFIRI, FOLTAX). This relationship is indicated by a “yes” or “no” response to the 
question: “Is there a reasonable possibility that the event may have been caused by 
IP and/or cytotoxic regimen?” 
 
The treating investigator (in communication with the PI) must assess whether the 
adverse event is possibly related to any study-mandated procedure or activity. This 
relationship is indicated by a “yes” or “no” response to the question: “Is there a 
reasonable possibility that the event may have been caused by a study procedure/ 
activity?” 
 
7.3.2  Serious Adverse Event Reporting 
 
All serious adverse events (as defined in section 7.3) occurring on this study require 
expedited reporting to the University of Chicago Comprehensive Cancer Center 
(UC CCC) Clinical Trials Office (CCTO).  The responsible Research Nurse or other 
designated individual should report the SAE to the CCTO by the end of the 

68 
 
business day when s/he becomes aware of the event.  Events occurring after 
business hours should be reported to the CCTO by 12pm (noon) the next business 
day.  Reports should be made using the eVelos database ‘Serious Event Report’ 
Form.   
 
All serious and unexpected adverse reactions must also be reported to the FDA.  
The responsible Research Nurse or other designated individual should provide a 
complete written report using the FDA MedWatch 3500A form.  The completed form 
should be sent to the CCTO at qaccto@bsd.uchicago.edu , within the specified 
timelines below regardless of whether all information regarding the event is 
available.  If applicable, a follow-up report should be provided to the CCTO if 
additional information on the event becomes available.   
 
Research staff (e.g. responsible research nurse) should NOT forward any adverse 
events directly to the FDA.  The CCTO will report all events to the FDA as per the 
current FDA guidelines.   
 
Fatal or Life-threatening Events: within 4 calendar days from treating investigator 
knowledge of the event 
 
All Other Reportable Events: within 10 calendar days of treating investigator 
knowledge of the event 
 
Any new information relating to a previously reported serious adverse event must 
be submitted to Amgen within 24 hours following knowledge of the new information. 
The investigator may be asked to provide additional follow-up information, which 
may include a discharge summary or extracts from the medical record. Information 
provided about the serious adverse event must be consistent with that recorded on 
the applicable CRF (eg, Adverse Event Summary eCRF). 
 
When required, events requiring anticipated protocol-specified procedures such as 
hospitalization for administration of chemotherapy, blood product transfusion, 
central line insertion, or disease progression of a primary tumor are exceptions to 
the reporting of serious adverse events. 
 
All serious adverse events should also be reported to the local IRB of record 
according to their policies and procedures.   
 
For patients receiving Rilotumumab: Amgen will be notified of pregnancy and 
lactation within 10 days of sponsor awareness. 
 
 
8. 
PHARMACEUTICAL INFORMATION 
 
8.1 
 Biologic Agents 
 
 
 
8.1.1 Trastuzumab  (Herceptin) 
 
 
This study will use commercially available Trastuzumab. For further details, see 
the current FDA approved Package Insert.  
 
 
 
8.1.2 MET Ab (TBD) 

69 
 
 
 
 
 
 
 
8.1.3 ABT806 
Abt-806 will be supplied by ABBVIE.  For further details see the current 
Investigator Brochure for the agent.   
 
 
 
8.1.4 FGFR2 ab (TBD) 
 
 
 
8.1.5 Nivolumab (Opdivo) 
 
This study will use commercially available Nivolumab. For further details, see 
the current FDA approved Package Insert.  
 
 
 
8.1.6 Ramucirumab (Cyramza) 
This study will use commercially available Ramucirumab. For further details, see 
the current FDA approved Package Insert.  
 
8.2 
Commercial Cytotoxic Agents 
 
           8.2.1    5-Fluorouracil/Leucovorin 
 
This study will use commercially available 5-Fluorouracil and leucovorin. For 
further details, see the local prescribing information for each agent. Treating 
physician has discretion upon use (or not) of the bolus 5FU/LV depending on 
clinical circumstances.  
 
          8.2.2    Oxaliplatin 
 
This study will use commercially available oxaliplatin. For further details, see the 
local prescribing information for each agent. 
 
 
 
 
 
8.2.3    Irinotecan 
 
This study will use commercially available irinotecan. For further details, see the 
local prescribing information for each agent. 
 
 
 
8.2.4    Docetaxel 
 
This study will use commercially available docetaxel. For further details, see the 
local prescribing information for each agent. 
 
 
9. 
BIOMARKER ASSESSMENT METHODS 
 
9.1 
Background and Algorithm 
Molecular profiling of tumors has led to the observation that although ‘driver-
oncogene’ aberrations can be determined with novel medium-high throughput 
assays,the various genomic aberrations are not necessarily mutually exclusive. 
One tumor sample may have up to 10 genomic aberrations.2,155 On average, we 
have observed ~3-5 genomic changes (mutations, amplifications, translocations) 
in GEC patients. Adding proteomic expression data to the genomic data adds 
another layer of complexity and ‘over-lapping’ of potential treatment categories. 

70 
 
Thus, in order to assign a patient to a predefined categorical molecular group 
that will be treated with one matched therapy, we have set a prioritization 
algorithm based on known clinical and preclinical information regarding the 
various potential molecular abnormalities (Figure 3, 6). Patients will be 
prioritized first by metastatic site if this is discordant from the primary tumor, then 
by prioritization as in Figure 3.  If patients are negative for all biomarkers, or a 
treatment assignment is unable to be obtained, patients are assigned to group 
#8 (Figure 3) with anti-angiogenesis ramucirumab. Assays used for biomarker 
assessment via the biomarker assessment and treatment algorithm are 
described in Section 2.5.  
 
 
 
  
 
9.2  Tissue Biomarker Assessment Methods156 
 
Assays used for biomarker assessment via the biomarker assessment and 
treatment algorithm are described in Section 2.5. These will be performed at 
diagnosis/enrollment on both the primary tumor sample and the metastatic 
lesion sample. (ie. If diagnostic biopsy is from the primary site, after enrollment 
patients will get a biopsy of a metastatic site or vice versa). The biomarker 
algorithm will be applied to both samples (primary/metastasis), and if 
discordant in terms of the results, biomarker classification and 
consequent recommended treatment assignment, the metastatic lesion 
will be prioritized and takes precedence.  
 
The assays will also be performed on serial biopsies taken of a 
progressing lesion each time of progression (PD1, PD2, PD3). The biomarker 
assay and treatment algorithm will be performed again at each time point, as 
described in Section 2.5.  While awaiting testing results, subjects should 
continue the current molecularly assigned therapy until results are 
available.  If a biopsy cannot be performed (eg if no safe lesion to biopsy is 
identified) or biopsy is inadequate and rebiopsy is not possible or also 
failed, ctDNA results may be applied to guide targeted therapy, and 
subjects should move to the next line of standard cytotoxic treatment 
(FOLFIRI or FOLTAX).  IF a patient withdraws consent for serial biopsy 
when possible during the trial, they will come off study and be treated with 
standard therapy. 
  
**Estimated # Biopsies: Baseline primary tumor, Baseline Metastatic 
Lesion, PD1, PD2, PD3 = 5. Biopsies obtained for other clinical reasons along 
with ctDNA NGS results may also be used to guide therapy at progression points 
if these are all that is available.  
 
9.2.1  Fluorescence in situ hybridization (FISH) 
 
 
 
 
9.2.1.1 HER2  
 
 
 
 
 
FISH for HER2 will be conducted in the University of Chicago CLIA certified 
Core Cytogenetics Laboratory in the Department of Pathology and scored per 
standard clinical HER2 FISH guidelines.71  This will be done as a routine 
diagnostic test (regardless of HER2 IHC results) prior to starting therapy, in 
order to determine HER2 status and eligibility for Trastuzumab therapy.  

71 
 
 
 
 
 
 
 
     
9.2.1.2 MET 
 
 
 
FISH for MET will be conducted a CLIA certified Core Cytogenetics Laboratory 
in the Department of Pathology or Clarient/Neogenomics, and scored per 
standard clinical HER2 FISH scoring guidelines for GEC.  
 
 
9.2.1.3 FGFR2 
 
 
 
FISH for FGFR2 will be conducted in the University of Chicago CLIA certified 
Core Cytogenetics Laboratory in the Department of Pathology or 
Clarient/Neogenomics, and scored per standard clinical HER2 FISH guidelines 
for GEC.  
 
 
9.2.1.4 KRAS 
 
       
 
 
 
FISH for KRAS may be conducted in the University of Chicago CLIA certified 
Core Cytogenetics Laboratory in the Department of Pathology or 
Clarient/Neogenomics, and scored per standard clinical HER2 FISH guidelines 
for GEC.  
 
 
9.2.1.5 MSI-H/EBV+/TMB>15mt/Mb/ PDL1+ CPS>10% 
 
 
NGS testing will include MSI status (MSI-H vs MSS) as well as tumor mutation 
burden (>15mt/Mb will be considered ‘high’). 
 
EBV testing will be conducted at the University of Chicago using routine clinical 
assay called Eber ISH.  
 
PDL1+ CPS>10% is scored with the routine FDA approved IHC 22C3 PharmDx 
assay 
  
 
 
9.2.1.6 EGFR 
 
 
 
FISH for EGFR will be conducted in the University of Chicago CLIA certified 
Core Cytogenetics Laboratory in the Department of Pathology or 
Clarient/Neogenomics, and scored per standard clinical HER2 FISH guidelines 
for GEC 
.  
9.2.2  Next-Generation Sequencing: Foundation One 
 
 
Next Generation Sequencing (NGS) will be performed using the medium 
throughput clinically available Foundation One test evaluating 315 oncogenes 
and tumor suppressors, and includes MSI-High testing and Tumor Mutation 
Burden Testing (TMB). This is a CLIA certified routinely ordered test. Results will 
be applied to the biomarker and treatment assignment algorithm, as described in 
section 2.5. 
 

72 
 
Circulating Tumor DNA (ctDNA) will be obtained throughout patient care using 
routine clinically available CLIA certified laboratory, Guardant Health with the 
Guardant360 assay. These ctDNA NGS results will be largely correlated with 
biopsy results as a correlative study, but these results will be used to direct 
targeted therapy if/when biopsy results are not obtainable/insufficient from 
metastatic/growing disease at baseline/progression.  
 
9.2.3  Immunohistochemistry 
 
 
 
 
9.2.3.1 HER2 
 
 
 
Immunohistochemistry for HER2 will be performed as a routine diagnostic test at 
the time of diagnosis per standard protocol (at the University of Chicago),  prior 
to starting therapy, in order to determine HER2 status and eligibility for 
Trastuzumab therapy.71 Results will be applied to the biomarker and treatment 
assignment algorithm, as described in section 2.5.  
 
PDL1+ CPS>10%. – will be performed as a routine diagnostic test at the time of 
diagnosis using the 22C3 PharmDx IHC assay.  
 
 
 
 
 
 
9.2.4   Mass Spectrometry: GEC-plex 
 
Mass Spectrometry (MS) will be performed (Oncoplex Dx) using the medium 
throughput clinically available GEC-plex test evaluating 15 peptides.119 Peptides 
include HER2, EGFR, HER3, MET, RON (3 peptides), FGFR1, FGFR2, KRAS 
(2 peptides), IGF1R, SRC, ROS1, PDL1, E-cadherin, Vimentin, and controls. 
This is a CLIA certified and routinely ordered test. Results will be applied to the 
biomarker and treatment assignment algorithm, as described in section 2.5.  
 
 
9.2.5   Collection, Handling, and Shipping of Specimens 
 
 
Collection of Tissue Specimens (see Appendix C) 
 
 This pilot phase study is being conducted at the University of Chicago.  
Specimens will be collected in the routine diagnostic manner following 
standard procedure, including from surgical, core needle, and endoscopic 
biopsies.   
 
 Patients will sign IRB protocol 16294A, the umbrella GI tissue and blood 
banking protocol, concurrently with the PANGEA consent.  
 
 Patients on anticoagulation will be bridged in the routine clinical 
manner usually followed for invasive procedures (using enoxaparin or 
other accepted clinical standard).  Warfarin is not allowed on protocol 
(see eligibility). 
 
 Specimens will be formalin fixed and paraffin embedded following routine 
pathologic procedures in of the Department of Clinical Pathology.  Routine 
diagnostic testing will be performed if there is yet to be an established 
diagnosis of cancer. If diagnosis is established, the obtained sample will be 
evaluated with one H&E slide to confirm adequate viability and percentage of 
tumor cells (>20%), as indicated in section 2.5.3 and Figure 3.   

73 
 
 
 One Core may be flash frozen and stored in the Catenacci laboratory for 
future use (eg. PAMGENE kinase activity analyses). 
 
 
 
 
 
 
Core Biopsies via Interventional Radiology (IR): 
 
 When obtaining Core biopsies, discussion with the research nurse and/or PI 
with Dr. Paul Chang or colleague in the Department of IR at UC will be done 
prior to each specified biopsy time point, based on most recent imaging, in 
order to determine the method (ultrasound or CT guided) and location (liver, 
lung, peritoneal etc) of biopsy to be conducted.  Safety of obtaining the 
biopsy will take precedence over the location. Every attempt will be 
made, however, to biopsy a progressing lesion (ie. that lesion felt most 
responsible for, or at least contributing to, progression by RECIST).  
 
An order for the biopsy will be placed as follows: 
 
“Core needle biopsy with 19 gauge (or less) needle. Please obtain at least 6 
core biopsies and process through routine diagnostic methods (formalin fix and 
send to diagnostic pathology). Please indicate ‘For molecular testing, require 
only H&E to confirm viable tumor. Please place the four cores in parallel on on 
FFPE block’ labeled on the sample. Please obtain an additional (at least 1) 
frozen core and page Leah Chase Clinical Research Associate for preparation of 
container and dry ice and pick up.” 
 
Leah Chase contact information: 
lmchase@medicine.bsd.uchicago.edu 
Pager:7918 
If not available paging the PI Dr. Catenacci p3044  
 
**The labeling on the biopsy sample, ‘For molecular testing, require only 
H&E to confirm viable tumor. Please place the six cores in parallel on 2 
FFPE blocks (3 cores each block)’ (see Appendix C), will indicate that only 
H&E staining should be done ONLY if diagnostic biopsies have ALREADY 
been obtained for the patient and a confirmed diagnosis is already 
available.  
 
The core biopsy that is frozen will be stored in the Catenacci laboratory at -80 
degrees Celsius for future studies.   
 
 
Handling, Allocation/Coordination, and Shipping of Specimens 
 
The specimens that are obtained and sent to pathology will be processed and 
assessed in the routine diagnostic manner. After diagnostic assessment of the 
percentage of viable tumor cells in the sample is completed by the pathologists 
(along with indicated tests including IHC HER2 and MET), the samples will be 
sent to central holding in Pathology. There, Venessa Perez (with Emily O’Day) 
will coordinate ordering, shipping, and retrieval of the FFPE blocks and 
the results to/from the University of Chicago Core Diagnostics 

74 
 
Laboratories and Quintiles Westmont (for IHC and FISH) and the other 
Commercial Diagnostics Laboratories (for Mass Spec and NGS) in the 
routine clinical manner (see Appendix C). Slides/tissue for testing on the 
blocks will be done in the following manner of prioritization: 
 
1. IHC HER2 (HER2 at U of C Department of Pathology)  
a. HER2 will be performed in the usual clinically indicated manner 
2. FISH HER2, MET, EGFR, KRAS, FGFR2 (Department of Pathology – 
Cytogenetics Laboratory) 
a. HER2 FISH will be performed in the usual clinically indicated 
manner 
b. MET, EGFR, KRAS, FGFR2 will be performed in the 
Cytogenetics laboratory via the laboratory developed test (LDT) 
and scoring methods.  
3. GEC-plex (Oncoplex Dx, Rockville, MD, USA) 
4. Foundation One (Foundation Medicine, Cambridge, MA, USA) Other 
commercial vendors for NGS may be considered if appropriate. 
 
Tissue will be saved by cutting fifteen 4uM sections for the planned IHC and 
FISH initially, at one time, as well as onto three 10uM laser capture 
microdissection (LCM) slides (Oncoplex Dx slides), to limit waste from facing the 
block several times, as we have previously demonstrated.1,2 An H&E will be 
done on the 1st and 15th 4uM slide cut. The three 10uM LCM slides and H&E 
(made from blank slide #15) will be sent to Oncoplex Dx for testing. The 
remaining FFPE tissue block will then be sent to Foundation Medicine. This will 
provide results from the four diagnostic modalities (IHC, FISH, MS, NGS) as 
efficiently and expediently as possible. The tissue remaining in the FFPE block 
will be returned to the University of Chicago and stored as is routinely done in 
the Department of Pathology.  Results from these studies will be applied to the 
biomarker assessment and treatment algorithm as delineated in Section 2.5 and 
Figure 3.  
 
9.3 
Blood Banking 
 
 
 
9.3.1   Collection of Specimens 
Serum, plasma, and whole blood will be collected at C1D1 and C4D1 of each 
line of therapy, and at last disease progression. This amounts to a maximum of 7 
draws per patient as below. 
Patients may sign IRB protocol 16294A, the umbrella GI tissue and blood 
banking protocol, concurrently with the PANGEA consent, and PANGEA consent 
allows for samples to be collected under 16294A (ie one or the other or both are 
equivalent for banking, but will be stored under the same IRB 16294A for 
parsimony purposes).  
All blood specimens MUST BE LABELED as follows: 
1. Patient name (Full first and last name) 
2. Medical record number 
3. Protocol number 
4. Date/time of blood draw 
5. Indication of the time point of the draw (ie OxC1D1, End of Study-EOS): 
i) 
OxC1D1 
ii) OxC4D1 
iii) IriC1D1 
iv) IriC4D1 

75 
 
v) TaxC1D1 
vi) TaxC4D1 
vii) EOS 
 
9.3.2   Handling of Specimens and Blood Banking 
   Blood will be collected as in 9.3.1, with one red top (serum), one green top 
(plasma) in 1ml aliquots and whole blood (one 10ml purple tops) for future 
analyses.  The purpose of such analysis will be to look at other potential 
biomarkers and relation to clinical outcomes.  Long term storage of samples (at 
least 5 years) will be at –80oC in the Phase I/GI Freezer space.  
 
9.4  
Shipping of Specimens 
Specimens will be shipped in the standard fashion to the outside clinical 
laboratories as in section 9.2.5 (Oncoplex Dx for Mass Spec, Foundation 
Medicine for Next-Generation Sequencing)  per routine care in coordination with 
the University of Chicago Department of Pathology. This will be coordinated by 
Venessa Perez (Pathology) and Leah Chase, pager 7918(email 
lmchase@medicine.bsd.uchicago.edu) as is routinely done for clinical samples 
for patients not enrolled in clinical trials. Upon completion of testing, the 
pathology slides and block will be returned to the University of Chicago 
Department of Pathology. 
 

76 
 
10.  STUDY CALENDAR 
 
Baseline evaluations are to be conducted within 14 days prior to start of study 
treatment.  Radiological scans must be done ≤4 weeks prior to the start of therapy, and 
it is preferred that the scans be done at the University of Chicago.  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. 
 
   
 
Pre- 
Study 
 
Wk 
1 
C1D1 
 
Wk
2 
Wk 
3 
C2D1
Wk 
4 
Wk 
5 
C3D1
Wk
6 
Wk 
7 
C4D1
Wk
8 
Wk 
9 G 
C5D1 
 
Wk 
10 
 
Wk 
11 
C6D1 
 
Wk 
12H
Off Study 
VisitE 
 
Biologic AgentA,K: 
i)Trastuzumab for HER2+ G 
ii) nivolumab for  
MSI-H/EBV+/TMB-High>15mt-
Mb/PDL1+ CPS>10% G 
iii) ABT-806 for EGFR+ G  
iv) Ramuciruamb for VEGFR2+ G 
 
 
 
 
X------------------------------------------------------------------------------------X 
 
                                                                             X---------------------X  
                                                                            X---------------------X 
                                                                           X---------------------X 
 
 
CytotoxicB Chemotherapy 
(ie. 1st, 2nd, 3rd line: 
i) 
mFOLFOX6 
ii) 
FOLFIRI,  
iii) FOLTAXL) 
 
 
 
X 
 
 
X 
  
X 
 
X 
  
X 
 
 
 
X 
 
 
 
 
Informed consent 
 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Medical history 
 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Concurrent meds 
 
X 
 
X-----------------------------------------------------------------------------------X 
 
 
Physical exam 
 
X 
 
X 
 
 
 
  
X 
 
 
 
X 
 
 
 
 
 
 
X 
 
Vital signs 
 
X 
 
X 
 
 
 
 
X 
 
 
 
X 
 
 
 
 
 
 
X 
 
Height 
 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Weight 
 
X 
 
X 
 
 
 
 
X 
 
 
 
X 
 
 
 
 
 
 
X 
 
Performance status 
 
X 
 
X 
 
 
 
 
X 
 
 
 
X 
 
 
 
 
 
 
X 
 
CBC w/diff, plts 
 
X 
 
X 
 
X 
X 
 
X 
 
X 
 
X 
 
 
 
X 
 
 
X 
 
Serum chemistryC 
 
X 
 
X 
 
X 
X 
 
X 
 
X 
 
X 
 
 
 
X 
 
 
X 
Ca 19-9 and CEAI 
 
    X  
 
X 
 
 
 
 
 
 
 
 
     X 
 
 
 
 
         X 
 
EKG  
 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Adverse event evaluation 
 
 
 
X---------------------------------------------------------------------------------X 
X 
 
 
Tumor measurements/ 
Radiologic evaluation with CT 
C/A/P infused 
 
 
XJ 
 
Tumor measurements are repeated every 8 weeks (4 cycles).  Radiologic 
documentation must be provided for patients removed from study for 
progressive disease.  *Patients should be re-evaluated for response 
every 8 weeks (2 months) irrespective of receiving all intended 
chemotherapy doses or delays.   
 
X 
 
MUGA or 2D cardiac ECHOD 
 
X 
 
  
 
 
 
 
  
 
 
 
  
 
 
 
 
 
X 
 
Biopsy/Tumor Blocks/slidesM (see 
section 9.2.5) 
 
X 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
XM (at PD1, 
PD2,PD3) 
Blood for correlativesF 
 
 
 
X 
 
 
 
 
 
 
X 
 
 
 
 
 
 
 
 
X 

77 
 
Opthalmology ExamN 
 X 
 
 
 
 
 
 
A: Biologic Agent:   
 
 
HER2 Positive: Trastuzumab 6 mg/kg IV C1D1 loading dose, then 4 mg/kg every cycle thereafter (every two weeks). 
 
MET Positive: Rilotumumab 10 mg/kg IV C1D1, every cycle thereafter (every two weeks). 
 
EGFR Positive: ABT-806 24 mg/kg IV C1d1, every cycle thereafter (every two weeks). See section 5.1.8 for premeds 
 
VEGFR2 Positive: Ramucirumab 8mg/kg IV C1D1, every cycle thereafter (every two weeks). 
 
B: Patients are treated with standard cytotoxic chemotherapy, as tolerated, and changed to second, third line therapy, as tolerated, upon 
i) disease progression, ii) intolerance to prior regimen (see Section 11 and 6, respectively).  
 
mFOLFOX6  
On day one of each treatment session patients will receive mFOLFOX6 with oxaliplatin 85 mg/m2 given as a two-hour 
intravenous (IV) infusion. The dose of leucovorin will remain fixed at 200 mg/m2 as a two-hour IV infusion followed by 5-
fluorouracil 400 mg/m2 IV push (bolus) and 5-fluorouracil 2400 mg/m2, given as a forty-six to forty-eight hour Infusion 
(Continuous Infusion).  
 
 
FOLFIRI 
FOLFIRI consists of 5-FU, leucovorin, and irinotecan. The dosing regimen for each subject will adhere to the protocol 
specifications. FOLFIRI dosing regimen will consist of l-LV 200 mg/m2 or dl-LV 400 mg/m2 as a 2-hour infusion, and irinotecan 
180 mg/m2 given as a 90-minute infusion in 500 mL dextrose 5% via a Y-connector, followed by bolus FU 400 mg/m2 and a 46-
hour infusion FU 2400 mg/m2. 
 
 
FOLTAX 
FOLTAX consists of 5-FU, leucovorin, and docetaxel. The dosing regimen for each subject will adhere to the protocol 
specifications. FOLTAX dosing regimen will consist of l-LV 200 mg/m2 or dl-LV 400 mg/m2 as a 2-hour infusion, and docetaxel 
50 mg/m2 given as a 90-minute infusion in 500 mL dextrose 5% via a Y-connector, followed by bolus FU 400 mg/m2 and a 46-
hour infusion FU 2400 mg/m2. 
 
 *5FU reductions (bolus and/or continous infusion) will carry over to second and third line therapy. 
 
C: Albumin, alkaline phosphatase, total bilirubin, bicarbonate, BUN, calcium, chloride, creatinine, glucose, potassium, total protein,  
SGOT [AST], SGPT [ALT], sodium. 
D: Echocardiogram or MUGA at screening for HER2 positive patients, to evaluate baseline cardiac ejection fraction. Repeat every 3 
months.  **If patients are not HER2 positive at baseline, but become HER2 positive at serial biopsy (ie PD1, PD2) and it is determined 
that the patient be treated with trastuzumab, a baseline study must be done at that time prior to commencing trastuzumab, to ensure 
EF>50%.  
E: Off-study evaluation within 30 days of last dose of therapy.   
F:   Blood collection and banking as in section 9.3, prior to administration of C1D1 and C1D4 of each line of chemotherapy and after last 
progression (ie PD3 or prior) for end of study sample, for a maximum of 7 blood draws throughout the trial.  The Blood Collection Form 
(Appendix A) is required for each sample collection to indicate the time point (eg OxC1D1, see Section 9.3.1) that the sample was 
acquired. *Patients will sign IRB protocol 16294A, the umbrella GI tissue banking protocol, concurrently. 
G.   Note that HER2 patients begin therapy with trastuzumab from C1D1 per clinical standards, if Her2 testing results available from the 
metastatic site,  
All other patients (HER2- will be treated with chemotherapy only (mFOLFOX6FOLFIRIFOLTAX) in the standard manner, until 
molecular profiling results become available at which time patients will be assigned and treated within the appropriate group. 
H.   The studies continue as indicated for each consecutive cycle until progression. At PD1 cytotoxic therapy is changed to second line 
FOLFIRI. At PD2, cytotoxic therapy is changed to FOLTAX. Assigned biologic agent continues beyond progression, unless repeat 
molecular testing suggests migration to a different molecular category, at which point the biologic therapy is changed to the appropriate 
new drug that matches the new molecular class – see protocol for further details. (see Section 5.1.2) 
I.      CEA Ca19-9 will be drawn at baseline and at least every two months with CT scans and at progression/off study evaluation. 
J.     Baseline CT for staging must be within 4 weeks of starting treatment, preferred at the University of Chicago. Baseline CT prior to 
starting off protocol treatment will be compared to the next CT and going forward, per RECIST, and included and assess as ORR1 best 
response evaluation.  
K.    Allow for up to 2 months for molecular testing when the molecularprofiling results become available.  
L.   Pre-med for the Docetaxel will premedicate with decadron 16mg/day (8mg twice daily) orally for 3 days, starting the day before docetaxel 
administration. 
M.   Biopsies through the course of therapy will be at the time of PD1 (first progression on FOLFOX), PD2 (second progression on FOLFIRI), 
and PD3 (third progression on FOLTAX). (See section 2.4, 2.4.4, and section 9) 
N.    Ophthalmology exam baseline for patients assigned to FGFR2 arm (drug TBD). 
 
* ALL lab tests, imaging, and treatment dosing may be done within a +/- 7 day 
window for holidays, weekends, unforeseen events (eg. inclement weather) 
and scheduling convenience. Routine labs may be drawn closer to home for 

78 
 
patient convenience. CTs and prospective tumor biopsies are preferred to be 
done at the University of Chicago Hyde Park Site.  
 
11.  MEASUREMENT OF EFFECT 
 
11.1 Antitumor Effect – Solid Tumors 
 
For the purposes of this study, patients should be re-evaluated for response 
every 8 weeks (2 months) irrespective of receiving all intended 
chemotherapy doses or delays.   
 
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). Changes in only the largest 
diameter (unidimensional measurement) of the tumor lesions are used in the 
RECIST criteria. 
 
11.1.1 
Definitions 
 
Evaluable for toxicity.  All patients will be evaluable for toxicity from the time of 
their first treatment on C1D1. 
 
Evaluable for objective response.  All registered patients will be considered 
evaluable for response by intention to treat. Subset analysis of patients receiving 
one or more doses will also be done.  These patients will have their response 
classified according to the definitions stated below and in section 13.  
 
11.1.2 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 >10 mm with CT scan, or >10 mm with 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 will not be 
considered measurable. 
 
Malignant lymph nodes.  To be considered pathologically enlarged and 
measurable, a lymph node must be >15 mm in short axis when assessed by 
CT scan (CT scan slice thickness recommended to be no greater than 5 mm).  
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 or pathological lymph nodes with ≥ 10 to <15 
mm 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. 
 

79 
 
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. Discussion with 
interventional radiology (Paul Chang and/or colleague) to determine the best 
baseline metastatic lesion (representative of disease, feasible/safe) to biopsy 
should be done, and this lesion that is ultimately biopsied included in the 
measurable lesions.   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.  
 
At disease progression by RECIST, or clinician’s discretion of clinical 
progression despite RECIST, another discussion with interventional radiology 
with ensue in order to determine best progression lesion to re-biopsy, and 
similarly the lesion that is ultimately biopsied included in RECIST calculation, if 
not already, moving forward. 
 
11.1.3  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. 

80 
 
 
Clinical lesions  Clinical lesions will only be considered measurable when they 
are superficial (e.g., skin nodules and palpable lymph nodes) and 10 mm 
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.  
 
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 or less.  If CT 
scans have slice thickness greater than 5 mm, 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).   
 
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. 
 
Ascites: 
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. 
 
If previous ascites and/or pleural effusion is stable by RECIST, but the effusion 
worsens and is amenable to therapeutic decompression, and the patient is 
otherwise tolerating therapy and otherwise clinically stable, the patient may be 
considered stable with final decision per discretion of the treating physician and 
PI. 
 
 
11.1.4  Response Criteria 
 
11.1.4.1  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. 
 
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 

81 
 
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.  (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 
 
11.1.4.2  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 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 
unequivocal progression of existing non-target 
lesions 
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). 
 
11.1.4.3  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. 
 
Target 
Lesions 
Non-Target 
Lesions 
New 
Lesions 
Overall 
Response
Best Response for this 
Category Also 
Requires: 
CR 
CR 
No 
CR 
>4 wks. Confirmation** 
CR 
Non-
CR/Non-PD 
No 
PR 
 
>4 wks. Confirmation** 
CR 
Not 
evaluated 
No 
PR 

82 
 
PR 
Non-PD/not 
evaluated 
No 
PR 
SD 
Non-PD/not 
evaluated 
No 
SD 
documented at least once 
>4 wks. from baseline** 
PD 
Any 
Yes or 
No 
PD 
 
no prior SD, PR or CR 
Any 
PD* 
Yes or 
No 
PD 
Any 
Any 
Yes 
PD 
* 
In exceptional circumstances, unequivocal progression in non-target lesions may be 
accepted as disease progression. 
**    Only for non-randomized trials with response as primary endpoint. 
 
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. 
 
 
11.1.5 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 recurrent 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.  
 
11.1.6  Progression-Free Survival 
 
PFS is defined as the duration of time from enrollment/registration to time of 
progression or death from any cause (PFS1+2+3). 
On this trial patients we will have up to three phases of treatment, as tolerated 
and indicated, as follows: 
 
PFS1: This, a secondary objective, is defined as the duration of time from 
enrollment/registration to time of progression on mFOLFOX6 chemotherapy and 
assigned biologicUpon first progression (PD1) by RECIST, patients change to 
second line therapy as tolerated. 
 
PFS2: This is defined as the duration of time from declaration of PD1 to time of 
progression on second line FOLFIRI chemotherapy and assigned biologic Upon 
second progression (PD2) by RECIST, patients change to third line therapy as 
tolerated. 
 
 
 
 
 
 
 
PFS3: This is defined as the duration of time from declaration of PD2 to time of 
progression on third line FOLTAX chemotherapy and assigned biologic.  Upon 
third/final progression (PD3) by RECIST, patients are removed from study. 

83 
 
 
 
 
 
11.1.7  Response Review 
 
Response rate is a secondary objective.  As above, RR at each line of therapy 
(RR1, RR2, RR3) will be recorded. In the event that patients are receiving 
mFOLFOX6 alone while molecular testing is being conducted and repeat 
imaging is performed, this will be denoted as RR0.  
 
11.2 Other Response Parameters and Objectives 
11.2.1 Overall survival, a primary objective, is defined as the duration of time 
from enrollment/registration to the time of death, of any cause.   
 
11.2.2 Toxicity, a secondary objective, is defined as in sections 6 and 7.  
 
11.2.3 Safety, a primary objective, will be assessed with respect to SAE due to 
baseline and serial biopsies. A rate of <5% SAE will be deemed acceptable for 
the a) elective baseline and b) serial biopsies, considered separately.  
Considering all enrolled patients (n=68), this will produce a 95% confidence 
width of approximately +/- 4.3% (+/-5.3% for the primary endpoint within the 
cohort of 68 patients undergoing study treatment) at for the baseline biopsy and 
the same for serial biopsies (this is a conservative estimate of precision given 
the possibility of multiple biopsies in each patient - up to 3).  Additionally, the 
safety lead-in of novel combinations of chemotherapy regimen with cytotoxic 
regimen will be followed, as in section 5.1.1.     
 
 
11.2.4 Feasibility, a primary objective, will be assessed and the trial deemed 
feasible if i) >85% of enrolled patients are successfully assigned, using our 
biomarker assessment and treatment assignment algorithm, by two 
months from biopsy; and ii) if >85% of enrolled patients have successful serial 
biopsy at first progression (PD1) and successful reassignment to biomarker 
group and matched treatment.  Considering all enrolled patients (n=68), this 
produces a 95% confidence width of approximately +/- 7% (+/-8.7% for the 
primary endpoint within the cohort of 68 patients) for the baseline biopsy and the 
same for serial biopsies (again, this is conservative given the possibility of 
multiple biopsies in each patient - up to 3). Patients can initiate cytotoxic therapy 
(FOLFOX) while awaiting biologic results/assignment, upon which the biologic is 
added to next cycle.  
 
12.  
DATA SAFETY REVIEW 
The PI will meet by teleconference with relevant pharmaceutical collaborators 
twice monthly during phase I safety lead-in (section 5.1.1) and at least monthly 
thereafter. Weekly meetings within the GI Oncology group will occur and review 
the previous week’s events, AEs, SAEs, and other pertinent information. The 
DSRC will be comprised of the study Principal Investigator, Dr. Catenacci and 
co-investigators of the study. 
 

84 
 
13.  
STATISTICAL CONSIDERATIONS 
 
13.1 Study Design/Endpoints 
 
Safety, a primary objective, will be assessed with respect to SAE due to baseline and 
serial biopsies. A rate of <5% SAE will be deemed acceptable for the a) elective 
baseline and b) serial biopsies, considered separately.  Considering all enrolled 
patients (n=104), this will produce a 95% confidence width of approximately +/- 4.3% 
(+/-5.3% for the primary endpoint within the cohort of 68 patients undergoing study 
treatment) at for the baseline biopsy and the same for serial biopsies (this is a 
conservative estimate of precision given the possibility of multiple biopsies in each 
patient - up to 3).  Additionally, the safety lead-in of novel combinations of 
chemotherapy regimen with cytotoxic regimen will be followed, as in section 5.1.1.     
 
 
 
Feasibility, a primary objective, will be assessed and the trial deemed feasible if i) 
>85% of enrolled patients are successfully assigned, using our biomarker assessment 
and treatment assignment algorithm, by two months from biopsy; and ii) if >85% of 
enrolled patients have successful serial biopsy at first progression (PD1) and 
successful reassignment to biomarker group and matched treatment.  Considering all 
enrolled patients (n=68), this produces a 95% confidence width of approximately +/- 
7% (+/-8.7% for the primary endpoint within the cohort of 68 patients) for the baseline 
biopsy and the same for serial biopsies (again, this is conservative given the 
possibility of multiple biopsies in each patient - up to 3).  
 
In addition to Safety and Feasibility, an efficacy primary endpoint (in addition to the 
safety and feasibility endpoints above and in 11.2.3 and 11.2.4) of this single arm pilot 
feasibility and exploratory ‘phase IIa’ pilot trial is median overall survival (mOS) of the 
all ITT categories combined, as defined in section 11.2.1.  The main analysis will be an 
intent-to-treat (ITT) analysis incorporating all screened patients included/enrolled into 
the study (N=68). 
    
A mOS time of approximately 12 months in gastric/gastroesophageal adenocarcinoma 
is observed historically, regardless of which first line and subsequent lines of 
chemotherapy used, including mFOLFOX6.14  This will be used as the estimated mOS 
This will require a total of approximately 68 patients. 
 
 
Survival time will be measured from the date of initial enrollment. We will estimate 
overall survival using the Kaplan-Meier (1958) method, and compare the observed 12-
month survival rate of the combined ITT targeted therapy categories to 50%, using a 
binomial test if there is no censoring, or a z-test based on the Greenwood standard 
error to accommodate censoring if necessary. Assuming mOS of 12 months in the 
historical control group, and 18 months in the personalized treatment approach 
(HR=0.67), and exponential survival, a total sample size of 68 subjects provides 80% 
power to detect a difference of this magnitude (63% 12-month survival rate), using a 
one-sided test at the 0.10 significance level. This assumes 24 month accrual period, 
subsequent 12 month follow-up period, with expected (H0) total events (death) of 34 
(0.50*68), compared to (H1) 25 ((1-0.63)*68), in this single arm exploratory study.  
 
*It is recognized that only 4 of 6 drugs are currently available for the proposed 
arms of personalized therapy. Notably, as molecular categories (FGFR2, MET) have 
yet to secure a drug for treatment, the initial iteration of the trial will be assessing the 
survival primary endpoint for only those treated by intention to treat the combined 

85 
 
HER2++, MSI-H/EBV+/TMB-High>15mt-Mb/PDL1+ CPS>10%, EGFR++/+, 
VEGFR2++/+ categories, along with the safety and feasibility endpoints. Patients who 
obtain anti-FGFR2 or anti-MET therapies will also be included in ITT analyses. For 
patients in any category initially without intended biologic therapy available, they will 
be treated with standard of care.  
 
 
On a rolling basis, as new drugs become available for the remaining vacant 
arms (ie. FGFR2, MET) ongoing enrollment of patients will be assigned to the 
appropriate therapy after amendment of the protocol has been approved to 
include the acquired agent.    
 
13.2 Sample Size/Accrual Rate 
 
The planned sample size will be 68 initial patients, as in section 13.1, for the per 
protocol ITT population (treated from the onset with appropriate targeted therapy).   
The primary endpoint is evaluating the personalized treatment strategy 
compared to historical control in this Type IIa Expansion Platform Clinical 
Trial Design.157 
 
13.3 Analysis of Secondary Endpoints 
 
13.3.1 Secondary endpoints 
 
 
 
Secondary endpoints will include mPFS and overall response rates (ORR) for the 
combined HER2++, - MSI-H/EBV+/TMB-High>15mt-Mb/PDL1+ CPS>10%, 
EGFR++/+, VEGFR2++/+ categories and any patient treated with antiFGFR2/MET 
during the course of the study (N=68), evaluated at each interval of therapy and 
total (1,2,3 and 1-3).  mPFS will be compared to historical controls of 6 months for 
mPFS1, 4 months for mPFS2, and 2 months for mPFS3. ORR will be compared to a 
historical control of 30% for ORR1, 20% for ORR2 and 10% for ORR3 using an 
exact binomial test.   
 
Adverse events will be summarized by type and grade and compared between 
groups using chisquare or Fisher exact tests, as appropriate. 
 
 
13.3.2 Subset Analyses between and within Molecular Categories  
 
A number of preplanned subset analyses will be performed. This is due to  
i) Inter-category variation. The varying prognostic implications of each molecular 
category (ie MET+ have worse prognosis than HER2+ with mOS of ~11.8 months 
for HER2+ versus 5.7 months for MET+ without matched biologic agent).   
ii) Intra-category variation. We will assess differences (exploratory) between HER2 
positive patients that are 2+ IHC/FISH+ and IHC3+/FISH+ as well as by Mass 
Spectrometry HER2+ expression. Similarly, for the MET+ category, this will consist 
of patients with MET amplification and consequent MET overexpression, as well as 
MET overexpression without gene amplification. These subgroups will be assessed 
individually in an exploratory and descriptive manner. The other subgroups will also 
be evaluated as such including but not limited to EGFR amplified versus EGFR 
overexpressing, KRAS amplified versus KRAS mutant versus relegation ‘not fitting 
into any other category’ (B9, Figure 3).  
 
 

86 
 
13.4  Reporting and Exclusions 
 
13.4.1  Evaluation of toxicity 
 
All patients will be evaluable for toxicity from the time of their first treatment with any 
biologic therapy.  Adverse events will be summarized by type and grade and 
compared between groups using chi-square or Fisher exact tests.   
 
 
13.4.2  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).   
 
All of the patients who met the eligibility criteria (with the possible exception of those 
who received no study medication) will be included in the main analysis of the 
response rate.  Patients in response categories 4-9 will be considered to have a 
treatment failure (disease progression).  Thus, an incorrect treatment schedule or 
drug administration will not result in exclusion from the analysis of the response 
rate.   
 
All conclusions will be based on all eligible patients.  Subanalyses will 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 will not serve as the basis for drawing conclusions concerning 
treatment efficacy, and the reasons for excluding patients from the analysis will be 
reported.   
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

87 
 
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96 
 
 
 
 
 
 
Appendix A 
The University of Chicago 
 
 
 
Blood Sample Collection Form 
 
PANGEA-IMBBP: Personalized ANtibodies for Gastro-Esophageal Adenocarcinoma -   
 
 
 
 
 
 
A 1st  Pilot Metastatic Trial of Biologics Beyond Progression  
 
 
Blood Banking:  i) Banking of  serum (1 red top), ii) plasma (1 green top), and iii) 
Whole Blood for DNA (1 purple top) for future studies 
 
Clinician/Research Nurse: Please Fill Out 
Blood Samples  
Patient Name: ___________________  Timpoint (eg OxC1D1 _________________ 
Patient Protocol ID #:______________  Date Blood Obtained: _________________ 
Date of Birth: _____________________Attending Physician: _________________ 
Visit 
 Collection Tubes to 
use: 
 
Date 
Drawn 
Processing  
Please check  
all samples collected        
OxC1D1   
 One 6ml Red (serum) Top 
One 6ml Green (plasma) Top 
One 10ml Purple  (whole blood) Tops 
 
Two 1 ml aliquots 
Two 1 ml aliquots 
No processing purple tops 
 
 
 
 
OxC4D1 
One 6ml Red (serum) Top 
One 6ml Green (plasma) Top 
One 10ml Purple  (whole blood) Tops  
 
Two 1 ml aliquots 
Two 1 ml aliquots 
No processing purple tops 
 
 
 
 
IriC1D1 
One 6ml Red (serum) Top 
One 6ml Green (plasma) Top 
One 10ml Purple  (whole blood) Tops  
 
Two 1 ml aliquots 
Two 1 ml aliquots 
No processing purple tops 
 
 
 
 
IriC4D1 
One 6ml Red (serum) Top 
One 6ml Green (plasma) Top 
One 10ml Purple  (whole blood) Tops  
 
Two 1 ml aliquots 
Two 1 ml aliquots 
No processing purple tops 
 
 
 
 
TaxC1D1 
One 6ml Red (serum) Top 
One 6ml Green (plasma) Top 
One 10ml Purple  (whole blood) Tops  
 
Two 1 ml aliquots 
Two 1 ml aliquots 
No processing purple tops 
 
 
 
 
TaxC4D1 
One 6ml Red (serum) Top 
One 6ml Green (plasma) Top 
One 10ml Purple  (whole blood) Tops  
 
Two 1 ml aliquots 
Two 1 ml aliquots 
No processing purple tops 
 
 
 
 
EOS 
One 6ml Red (serum) Top 
One 6ml Green (plasma) Top 
One 10ml Purple  (whole blood) Tops  
 
Two 1 ml aliquots 
Two 1 ml aliquots 
No processing purple tops 
 
 
 
 
PANGEA 
IRB# 14‐0141 

97 
 
APPENDIX B 
 
ACCEPTABLE AND UNACCEPTABLE FORMS OF CONTRACEPTION FOR WOMEN 
OF CHILDBEARING POTENTIAL 
 
 
Women of childbearing potential are required to use two forms of acceptable 
contraception, including one barrier method during participation in the study and for the 12 
months following the last dose. 
 
Acceptable forms of contraception for women of childbearing potential: 
Primary Forms 
 Tubal ligation 
 Partner’s vasectomy 
 Intrauterine device 
 Hormonal (combination birth control pills, skin patches, injections, implants, or 
vaginal ring) 
 Barrier forms (always used with spermicide) 
 
Secondary Forms 
 Diaphragm 
 Cervical cap 
 Barrier form (used with or without spermicide) 
 Male latex condom 
 Vaginal sponge (contains spermicide) 
 
Unacceptable forms of contraception for women of childbearing potential: 
 Birth control pills without estrogen 
 IUD progesterone T 
 Female condom 
 Natural family planning (i.e., rhythm method) or breastfeeding 
 Fertility awareness 
 Withdrawal 
 Cervical shield 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

98 
 
APPENDIX C 
 
COLLECTION OF TISSUE SPECIMENS ALGORITHM