Molecular-guided Therapy for the Treatment of Patients With Relapsed and Refractory Childhood Cancers
Phase: NA
Conditions: Neuroblastoma, Medulloblastoma, Glioma, Ependymoma, Choroid Plexus Neoplasms, Craniopharyngioma, Dysembryoplastic Neuroepithelial Tumor, Meningioma, Primitive Neuroectodermal Tumors (PNETs), Germ Cell Tumors, Rhabdomyosarcoma, Non-rhabdomyosarcoma, Ewings Sarcoma, Osteosarcoma, Wilms Tumor, Renal Cell Carcinoma, Malignant Rhabdoid Tumor, Clear Cell Sarcoma, Liver Tumors
Sponsor: Giselle Sholler

Clinical Protocol NMTRC009 
 
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Protocol NMTRC009 
 
 
 
 
 
Molecular-guided therapy for the treatment of patients with relapsed and refractory 
childhood cancers 
 
 
 
 
 
 
Version 3.0    January 10, 2017  
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Clinical Protocol NMTRC009 
 
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Contact Information: 
 
STUDY CHAIR: 
 
Giselle Sholler, MD 
NMTRC Chair 
100 Michigan Avenue NE  MC 272         
Grand Rapids, MI 49503 
Tel:  (616) 267-0332  
Fax: 616-391-2785 
giselle.sholler@helendevoschildrens.org 
 
 
 
 
 
STUDY VICE CHAIR:  
 
Jeff Trent 
Translational Genomics Research Institute (TGen)  
President and Research Director 
445 N 5th Street 
Phoenix, AZ 85004 
602-343-8419  
jtrent@tgen.org 
       
 
 
 
 
 
 
 
Safety Officer:  
 
 
Melinda Merchant, PhD, MD 
AstraZeneca 
Senior Medical Director, Oncology 
Translational Medical Unit 
Early Clinical Development 
35 Gatehouse Dr, Waltham MA 02451 
Tel: +1 781-491-5292 
melinda.merchant@astrazeneca.com 
 
 
 
 
 
 

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STUDY COMMITTEE MEMBERS: 
 
Genevieve Bergendahl, RN 
Clinical Program Director 
NMTRC 
100 Michigan Avenue NE  MC 272         
Grand Rapids, MI 49503 
 
Tel:  (616) 267-0335 
Fax: 616-391-2785 
E-Mail:  
Genevieve.bergendahl@helendevoschildrens.org  
 
 
Alyssa VanderWerff 
Clinical Program Coordinator 
NMTRC 
100 Michigan Avenue NE  MC 272         
Grand Rapids, MI 49503 
 
Tel:  (616) 267-0327  
Fax: 616-391-2785 
E-Mail:  
Alyssa.VanderWerff@helendevoschildrens.org  
 
 TBDClinical Project Coordinator 
NMTRC 
100 Michigan Avenue NE  MC 272         
Grand Rapids, MI 49503 
 
Tel:  (616) 391-0807 
Fax: 616-391-2785 
E-Mail:  
  
Abhinav Beeravally Nagulapally 
Computational Biologist 
NMTRC 
100 Michigan Avenue NE  MC 272         
Grand Rapids, MI 49503 
 
Tel:  (616) 267-0346 
Fax: 616-391-2785 
E-Mail: 
Abhinav.BeeravallyNagulapally@helendevosc
hildrens.org 
William Ferguson, MD  
 
 
Pediatric Hematology-Oncology 
 
Cardinal Glennon Children’s Medical Ctr  
Saint Louis University School of Medicine 
1465 S. Grand Blvd. 
St. Louis, MO 
Tel:  
(314) 577-5638 
Fax:  
(314) 268-4081 
fergusws@slu.edu 
 
 
William Roberts, MD 
 
 
 
Pediatric Hematology/Oncology  
 
Rady Children's Hospital San Diego  
 
3020 Children’s Way MC5035 
San Diego, CA 92123-4282 
 
Tel:  
(858) 966-5811 
Fax:  
(858) 966-8035 
wroberts@chsd.org 
 
Don Eslin, MD 
Arnold Palmer Hospital for Children 
Pediatric Hematology/Oncology 
50 W. Sturtevant St. 
Orlando, FL 32806 
Tel: 321-841-8588 
Don.Eslin@orlandohealth.com 
 
 

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Jacqueline Kraveka, DO 
 
 
 
 
Medical University of South Carolina 
 
Division of Pediatric Hematology-
Oncology 
135 Rutledge Avenue, Room 489 
MSC 558 
Charleston, SC 29425 
Tel: 843-792-2957 
Fax: 843-792-8912 
kravekjm@musc.edu 
 
Amy Lee Bredlau, MD 
Director, Pediatric Brain Tumor Program 
Assistant Professor, Sullivan Scholar 
Medical University of South Carolina 
135 Rutledge Avenue, MSC 558 
Charleston, SC 29425 
Phone: 843-876-2872 
Fax: 843-792-8912 
bredlau@musc.edu  
Javier Oesterheld, MD 
Levine Children’s Hospital 
 
1000 Blythe Blvd 
 
 
Charlotte, NC 282033 
Tel: 704-381-9900 
Fax: 704-381-9901 
Javier.oesterheld@carolinashealthcare.org  
 
Deanna Mitchell, MD  
 
 
Michigan State University 
 
 
Helen DeVos Children’s Hospital 
100 Michigan NE 
Grand Rapids, MI 49503 
Tel: 616-391-2086 
Deanna.Mitchell@ helendevoschildrens.org  
 
Micheal Isakoff, MD 
 
Assistant Professor of Pediatrics  
 
Connecticut Children's Medical Center  
Division of Hematology / Oncology 2J 
282 Washington Street 
Hartford, CT 06106 
 
Tel: 860-545-9630 
Fax: 860-545-9622 
Misakoff@connecticutchildrens.org  
 
 
 
Kathleen Neville, MD, MS 
Arkansas Children’s Hospital 
Director, Experimental Therapeutics in 
Pediatric Oncology Program 
Associate Professor of Pediatrics 
1 Children’s Way; Slot 512-23 
Little Rock, AR 72202 
 
Office: (501)364-4405kaneville@uams.edu  
Randal K. Wada, MD 
Associate Professor of Pediatrics and 
Nursing 
University of Hawaii 
Kapiolani Medical Center for Women and 
Children  
55 Merchant Street, 26th Floor 
Honolulu, HI 96813 
 
Office/Lab: (808) 586-2963 
randalw@hawaii.edu   

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Francis Eshun, MD 
Center for Cancer and Blood Disorders 
Phoenix Children's Hospital 
1919 Thomas Road 
Phoenix, AZ 85016 
 
 
feshun@phoenixchildrens.com 
602-933-0920 
 
Devang Pastakia, MD 
Vanderbilt-Ingram Cancer Center 
397 Preston Research Building 
2220 Pierce Ave 
Nashville, TN 37232 
Phone: 615-875-6129 
Email: devang.pastakia@Vanderbilt.Edu  
 
 
Virginia Harrod MD, PhDChief-Neuro-
OncologyDell Children's Blood and Cancer 
Center 
1301 Barbara Jordan Blvd, Ste 401 
Austin,  Texas   78723 
 
512-628-1900    office 
VLHarrod@seton.org 
Mark Fluchel, MD 
Primary Children's Hospital 
Division of Pediatric 
Hematology/Oncology 
100 North Mario Capecchi Drive, 4th Floor 
Salt Lake City, UT 84113 
 
Phone: 801-662-4700 
Fax: 801-662-4705 
email: mark.fluchel@imail.org 
 
Valerie I. Brown, MD, PhD 
Associate Professor of Pediatrics 
Division of Pediatric 
Oncology/Hematology 
Clinical Director, Experimental 
Therapeutics 
Attending Physician, Hematopoietic Stem 
Cell Transplant Program 
Penn State Milton S. Hershey Medical 
Center and Children’s Hospital 
500 University Dr. 
P.O. Box 850, MC H085 
Hershey, PA  17033-0850 
 
Phone: 717-531-1042 
Email: vbrown1@hmc.psu.edu 
 
 
Daniel Marc Rubin ND FABNO 
Medical Director 
Naturopathic Specialists, LLC 
7331 E Osborn Dr  
Suite 330 
Scottsdale, AZ 85251 
 
Phone: 480-990-1111 
email: rubinhere@me.com 
 

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Jeffrey Bond, PhD 
 
 
 
NMTRC 
100 Michigan Avenue NE  MC 272         
Grand Rapids, MI 49503 
 
Tel:  
(802) 656-4608 
jeffrey.bond@ helendevoschildrens.org 
 
Gina K. Hanna, PharmD 
Pediatric Oncology Clinical Trials 
Pharmacist 
Dana-Farber Cancer Institute  
Yawkey Center for Cancer Care 
Research Pharmacy  Y-5 | 450 Brookline 
Ave | Boston, MA  02215 
 
phone 617.582.8125 | fax 617.632.4616 
ginak_hanna@dfci.harvard.edu  
Meghan M. Devine, PharmD 
Clinical Specialist, Pediatric Hematology 
and Oncology 
Pharmacy Services-Levine Children's 
Hospital at Carolinas Medical Center 
1000 Blythe Blvd 
Charlotte, NC 28203 
 
Phone: 704-381-7049 
Meghan.Devine@carolinashealthcare.org 
 
Jeff Trent 
Translational Genomics Research Institute 
(TGen) President and Research Director 
445 N 5th Street 
Phoenix, AZ 85004 
602-343-8419  
 jtrent@tgen.org 
            
Matt Huntelman 
Translational Genomics Research Institute 
(TGen) Associate Professor, 
Neurogenomics Division 
445 N 5th Street 
Phoenix, AZ 85004 
602-343-8730      
mhuentelman@tgen.org 
 
John Carpten 
Translational Genomics Research Institute 
(TGen) Deputy Director of Basic Science 
445 N 5th Street 
Phoenix, AZ 85004 
602-343-8819  
jcarpten@tgen.org 
                                               
Jeff Keifer 
Translational Genomics Research Institute 
(TGen) Research Associate Professor 
445 N 5th Street 
Phoenix, AZ 85004 
602-343-8667  
jkiefer@tgen.org 

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David Craig 
Translational Genomics Research Institute 
(TGen)  
Deputy Director, Informatic Sciences and 
Professor and Director, Neurogenomics 
Division  
445 N 5th Street 
Phoenix, AZ 85004 
602-343-8747 
dcraig@tgen.org 
William Burleson 
Translational Genomics Research Institute 
(TGen)  
Product Delivery Manager  
445 N 5th Street 
Phoenix, AZ 85004 
602-343-8503 
wburleson@tgen.org 
Apurva Patel 
Translational Genomics Research Institute 
(TGen)  
Director, Enterprise Applications  
445 N 5th Street 
Phoenix, AZ 85004 
602-343-8404 
apatel@tgen.org 
Janine LoBello, DO 
Ashion Analytics, LLC 
Laboratory Director 
445 N 5th Street 
Phoenix, AZ 85004 
602-343-8606 
jlobello@ashiondx.com 
 
 

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INVESTIGATOR SIGNATURE SHEET 
 
I have read the attached protocol amendment and agree that it contains all the necessary details 
for performing the study. 
 
I will review copies of the amended protocol and of the preclinical and clinical information on the 
test article, which was furnished to me by the Sponsor, to all members of the study team 
responsible to me who participate in the study.  I will discuss this material with them to assure 
that they are fully informed regarding the test article and the conduct of the study. 
 
Once the protocol has been approved by the Institutional Review Board (IRB)/Independent Ethics 
Committee (IEC), I will not modify this protocol without obtaining the prior approval of the 
Sponsor and of the IRB/IEC.  I will submit the protocol modifications and/or any informed 
consent form (ICF) modifications to the Sponsor and the IRB/IEC, and approval will be obtained 
before any modifications are implemented. 
 
I understand the protocol and will work according to it, the principles of Good Clinical Practice 
(GCP) [current International Conference of Harmonization (ICH) guidelines], and the Declaration 
of Helsinki (1964) including all amendments up to and including the Scotland revision (2000) and 
notes of clarification added in 2002 and 2004. 
 
 
 
 
 
Investigator's Signature 
 
Date 
 
 
 
Investigator’s Printed Name 
 
 
 
 
 
Investigational Site Name 
 
 
 
 
 
 
 
 
 
 
 

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TABLE OF CONTENTS 
 
Contact Information: ________________________________________________________ 2 
TABLE OF CONTENTS _____________________________________________________ 9 
PROTOCOL SYNOPSIS ___________________________________________________ 12 
TABLE OF PROCEDURES AND ASSESSMENTS _____________________________ 19 
 
1 
Background ______________________________________________________ 20 
1.1 Study Disease ________________________________________________ 20 
1.2 Rationale____________________________________________________ 20 
 
2 
STUDY OBJECTIVES _____________________________________________ 25 
2.1 Primary Objectives ____________________________________________ 25 
2.2 Secondary Objectives __________________________________________ 25 
2.3 Subject Enrollment and Sample Procurement and Data Processing ____ 25 
2.4 DNA and RNA Sequencing _____________________________________ 26 
2.5 NMTRC Drug prediction report _________________________________ 27 
 
3 
Treatment Protocol Decision _________________________________________ 30 
3.1 Decision Making Rules for Treatment Regimens ____________________ 30 
3.2 Additional Biopsies: ___________________________________________ 32 
3.3 Safety Evaluations ____________________________________________ 32 
3.4 Efficacy Evaluations __________________________________________ 33 
3.5 Biological Studies _____________________________________________ 33 
3.6 Treatment during waiting period _________________________________ 33 
 
4 
SUBJECT SELECTION ____________________________________________ 33 
4.1 Inclusion Criteria _____________________________________________ 33 
4.2 Exclusion Criteria ____________________________________________ 36 
 
5 
STUDY PROCEDURES AND ASSESSMENTS _________________________ 36 
5.1 Enrollment of Subjects_________________________________________ 36 
5.2 Screening ___________________________________________________ 37 
5.3 Study Procedures/Study Interventions ____________________________ 38 
 

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6 
Protocol Drugs ____________________________________________________ 41 
6.1 Treatment modifications _______________________________________ 41 
6.2 Concomitant Medications and Treatments _________________________ 41 
 
7 
Efficacy Assessments _______________________________________________ 42 
7.1 Tumor Assessments/Scans ______________________________________ 42 
7.2 Scan Submission: _____________________________________________ 42 
7.3 Response Criteria _____________________________________________ 42 
 
8 
Sample Size Justification ____________________________________________ 44 
 
9 
Laboratory Evaluations _____________________________________________ 45 
9.1 Specimens to be Collected, Schedule and Amount ___________________ 45 
9.2 Tumor collection and correlative biology studies. ___________________ 45 
9.3 Detailed Procedure For Sending Subject Samples: __________________ 46 
9.5 Storage _____________________________________________________ 50 
9.6 Plan for Communication of Samples and Data _____________________ 51 
9.7 Plan for Communication of Collaborating Sites ____________________ 52 
 
10 ADVERSE EVENT REPORTING ____________________________________ 52 
10.1 Definitions _________________________________________________ 52 
10.1.4 Documenting Adverse Events _________________________________ 53 
10.1.5 Expedited Reporting of Serious Adverse Events __________________ 54 
10.1.6 Grading and Relatedness of Adverse Events _____________________ 54 
 
 
11 SUBJECT WITHDRAWAL AND TRIAL DISCONTINUATION ___________ 56 
11.1 Criteria for Subject Off-Therapy ________________________________ 56 
11.2 Criteria for Subject Off-Study __________________________________ 56 
11.3 Trial Discontinuation _________________________________________ 56 
 
12 DATA ANALYSIS _________________________________________________ 56 
12.1 Data Quality Assurance _______________________________________ 56 
12.2 Data Safety Monitoring Board (DSMB) __________________________ 57 

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12.3 Process and Feasibility Analysis ________________________________ 57 
12.4 Secondary Data Analysis ______________________________________ 57 
 
13 ADMINISTRATIVE PROCEDURES _________________________________ 57 
13.1 Subject Informed Consent _____________________________________ 57 
13.2 Ethical Conduct of the Study and IRB/IEC Approval _______________ 58 
13.3 Monitoring _________________________________________________ 58 
13.4 Pre-Study Documentation _____________________________________ 59 
13.5 Confidentiality ______________________________________________ 59 
13.6 Source Documents ___________________________________________ 59 
13.7 Record Retention ____________________________________________ 60 
 
References ________________________________________________________________ 61 
 
Appendix I: Performance Status/Scores _______________________________________ 64 
 
Appendix II: Biology Studies Collection and Shipping forms ______________________ 65 
 
Appendix III: Pharmacopeia Library _________________________________________ 67 
 
Appendix IV- Example expression file format for the VCF 4.1: ____________________ 69 
 
 
 
 
 

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PROTOCOL SYNOPSIS 
PROTOCOL TITLE 
Molecular-guided therapy for the treatment of patients with relapsed 
and refractory childhood cancers 
PROTOCOL NUMBER 
NMTRC009 
PHASE OF DEVELOPMENT Feasibility 
OBJECTIVES 
Primary 
Determine feasibility of using tumor samples to assess genomic 
sequencing using predictive modeling to make real-time treatment 
decisions for children with relapsed/refractory cancers 
 
Secondary 
• To determine the activity of treatments chosen based on: 
• 
Overall response rate (ORR)  
• 
Progression free survival (PFS)  
• To continue to evaluate the safety of allowing a molecular tumor 
board to determine individualized treatment plans 
• (Voluntary) 
To 
explore 
the 
relationship 
between 
tumor 
phenotype/genotype and response by permitting use of tumor tissue 
in a correlative biologic study 
• To compare PFS interval to PFS intervals of previous 
chemotherapy regimens since relapse for each subject. 
• Sub analysis examination of disease types. 
STUDY DESIGN 
A prospective open label, multicenter study to evaluate the feasibility 
of molecularly guided therapy in patients with relapsed or refractory 
childhood cancers 
 
A total of 200 evaluable subjects with childhood cancer that are 
refractory to or have relapsed on conventional therapy will be treated 
with molecular guided therapy. Additional patients may enroll through 
compassionate access if no other treatment options are available. 
 
Subjects will be evaluated in 3 strata: 
• 
Stratum 1: 50 subjects with refractory/relapsed neuroblastoma 
• 
Stratum 2: 50 subjects with relapsed or refractory brain tumors 
• 
Stratum 3: 100 subjects with refractory or relapsed rare tumors 
 
Guided therapy will allow the use of individualized therapeutic 
combinations (up to 4 agents). All subjects will be followed for 
survival, disease response, progression and safety.  All subjects will be 
treated according to the discretion of the treating oncologist and study 
committee (minimum 3 oncologists and one pharmacist). Extent of 
disease will be measured and assessed for changes throughout the 
course of the study.  

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ELIGIBILITY 
Inclusion Criteria 
1. Subjects must have proven pediatric cancer with confirmation at 
diagnosis or at the time of recurrence/progression and clinical 
determination of disease for which there is no known effective 
curative therapy or disease that is refractory to established proven 
therapies fitting into one of the following categories: 
a. Neuroblastoma- Patients that have relapsed following 
standard of care therapy (such as high risk patients, patient 
presenting after age 15 months or MYCN amplified, and only 
following (for eligible patients) high-dose chemotherapy 
followed by hematopoietic stem cell transplantation and 
maintenance therapy with retinoic acid and antibody therapy) 
or having progressed during standard of care therapy and non-
responsive/progressive to accepted curative chemotherapy. 
b. Brain Tumors 
i. Medulloblastomas (At relapse after standard of care 
therapy [surgery, chemotherapy and/or radiation] 
and/or 
non-responsive/progressive 
on 
accepted 
curative therapy) 
ii. Gliomas (At relapse after standard of care therapy 
[surgery and/or radiation and/or chemotherapy] and/or 
non-responsive/progressive on accepted curative 
therapy) 
iii. Diffuse 
Intrinsic 
Pontine 
Glioma/DIPG/Diffuse 
Midline Tumor- (At diagnosis, as there is no known 
curative therapy) 
iv. Glioblastoma Multiforme- (At diagnosis, as there is 
no known curative therapy) 
v. Ependymomas (At relapse after standard of care 
therapy [surgery with or without radiation] and/or 
non-responsive/progressive on accepted curative 
therapy) 
vi. Choroid plexus tumors (At relapse after standard of 
care 
therapy 
[surgery] 
and/or 
non-
responsive/progressive on accepted curative therapy) 
vii. Craniopharyngiomas (At relapse after standard of care 
therapy [surgery or suppressive therapy] and/or non-
responsive/progressive on accepted curative therapy) 
viii. Dysembryoplastic neuroepithelial tumors (DNETs) 
(At relapse after standard of care therapy [surgery] 
and/or 
non-responsive/progressive 
on 
accepted 
curative therapy) 
ix. Meningiomas (At relapse after standard of care 
therapy [surgery] and/or non-responsive/progressive 
on accepted curative therapy) 
x. Primitive Neuroectodermal Tumors (PNETs)/CNS 
Embryonal Tumors (At relapse after standard of care 
therapy [surgery, chemotherapy, and/or radiation] 
and/or 
non-responsive/progressive 
on 
accepted 

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curative therapy) 
xi. Germ cell tumors (At relapse after standard of care 
therapy 
[surgery, 
and/or 
radiation 
and/or 
chemotherapy] and/or non-responsive/progressive on 
accepted curative therapy) 
xii. Atypical Teratoid Rhabdoid Tumor (ATRT) (At 
relapse after standard of care therapy [surgery, 
chemotherapy 
and/or 
radiation] 
and/or 
non-
responsive/progressive on accepted curative therapy) 
c. Rare Tumors: 
i. Soft tissue sarcoma 
Rhabdomyosarcoma (At relapse after standard of care 
therapy [surgery, and/or radiation, chemotherapy] 
and/or 
non-responsive/progressive 
to 
accepted 
curative chemotherapy) 
Non-rhabdomyosarcoma (At relapse after standard of 
care 
therapy 
[surgery, 
and/or 
radiation, 
chemotherapy] and/or non-responsive/progressive to 
accepted curative chemotherapy) 
ii. Bone 
Ewings sarcoma (At relapse after standard of care 
therapy [surgery, and/or radiation, chemotherapy] 
and/or non- responsive/progressive to accepted 
curative chemotherapy) 
Osteosarcoma (At relapse after standard of care 
therapy 
[surgery, 
chemotherapy] 
and/or 
non- 
responsive/progressive 
to 
accepted 
curative 
chemotherapy) 
iii. Renal 
Wilms tumor (At relapse after standard of care 
therapy [surgery, and/or radiation, chemotherapy] 
and/or non- responsive/progressive to accepted 
chemotherapy) 
Renal cell carcinoma (At relapse after standard of care 
therapy 
[surgery, 
chemotherapy] 
and/or 
non- 
responsive/progressive 
to 
accepted 
curative 
chemotherapy) 
Malignant rhabdoid tumor (At diagnosis, as there is 
no known curative therapy) 
Clear Cell Sarcoma- (At relapse after standard of care 
therapy 
[radiation, 
chemotherapy] 
and/or 
non- 
responsive/progressive 
to 
accepted 
curative 
chemotherapy) 
iv. Germ Cell tumors (At relapse after standard of care 
therapy 
[surgery, 
chemotherapy] 
and/or 
non-
responsive/progressive 
to 
accepted 
curative 
chemotherapy) 
v. Liver Tumors (At relapse after standard of care 
therapy 
[surgery, 
chemotherapy] 
and/or 
non- 

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responsive/progressive 
to 
accepted 
curative 
chemotherapy)   
vi. Carcinomas- (At relapse after standard of care therapy 
and/or non- responsive/progressive to accepted 
curative chemotherapy)   
vii. Desmoid tumors- (At relapse after standard of care 
therapy 
and/or 
non- 
responsive/progressive 
to 
accepted curative chemotherapy)   
viii. Malignant 
Peripheral 
Nerve 
Sheath 
Tumors 
(MPNST)- (At diagnosis, as there is no known 
curative therapy).  
ix. Pheochromocytoma (At relapse after standard of care 
therapy 
and/or 
non- 
responsive/progressive 
to 
accepted curative chemotherapy).   
x. Ethesioneuroblastoma (At relapse after standard of 
care therapy and/or non- responsive/progressive to 
accepted curative chemotherapy). 
xi. Neuroendocrine tumors (At relapse after standard of 
care therapy and/or non- responsive/progressive to 
accepted curative chemotherapy). 
xii. Desmoplastic small round cell tumor (At relapse after 
standard of care therapy and/or non- 
responsive/progressive to accepted curative 
chemotherapy). 
xiii. Melanoma (At relapse after standard of care therapy 
and/or non- responsive/progressive to accepted 
curative chemotherapy). 
2. Subjects must be age >12 months at enrollment 
3. Subjects must be age  ≤ 21 years at initial diagnosis  
4. Subjects must have measurable disease as defined by RESIST 
v1.1 at the time of biopsy and tumor must be accessible for 
biopsy. Tumor samples submitted for analysis must contain >50% 
viable tumor tissue to qualify. In addition, subjects with disease 
confined to the bone marrow are eligible to enroll if the degree of 
marrow involvement is expected to be >50%. 
Note: Subjects who are expected to have no evidence of disease 
after surgical removal of their tumor are still eligible for this trial if 
their disease would normally require adjuvant chemotherapy 
treatment after surgery despite NED status.  
5. Current disease state must be one for which there is currently no 
known effective therapy 
6. Specimens will be obtained only in a non-significant risk manner 
and not solely for the purpose of investigational testing. 
7. Lansky or Karnofsky Score must be ≥ 50 
8. Subjects without bone marrow metastases must have an ANC > 

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750/μl to begin treatment. 
9. Subjects with CNS disease currently taking steroids must have 
been on a stable dose of steroids for 2 weeks prior to their biopsy 
and must not have progressive hydrocephalus at enrollment.  
10. Adequate liver function must be demonstrated, defined as: 
a. Total bilirubin ≤ 1.5 x upper limit of normal (ULN) for age 
AND 
b.  ALT (SGPT) < 10 x upper limit of normal (ULN) for age 
11. A negative serum pregnancy test is required for female 
participants of child bearing potential (≥13 years of age or after 
onset of menses) 
12. Both male and female post-pubertal study subjects need to agree 
to use one of the more effective birth control methods during 
treatment and for six months after treatment is stopped. These 
methods include total abstinence (no sex), oral contraceptives 
(“the pill”), an intrauterine device (IUD), levonorgestrol implants 
(Norplant), or medroxyprogesterone acetate injections (Depo-
provera shots). If one of these cannot be used, contraceptive foam 
with a condom is recommended. 
13. Informed Consent: All subjects and/or legal guardians must sign 
informed written consent. Assent, when appropriate, will be 
obtained according to institutional guidelines 
 
 
Exclusion Criteria 
14. Subjects who have received any cytotoxic chemotherapy within 
the last 7 days prior to biopsy  
15. Subjects who have received any radiotherapy to the primary 
sample site within the last 14 days (radiation may be included in 
treatment decision after biopsy). 
16. Subjects receiving any investigational drug concurrently. 
17. Subjects with uncontrolled serious infections or a life-threatening 
illness (unrelated to tumor) 
18. Subjects 
with 
any 
other 
medical 
condition, 
including 
malabsorption syndromes, mental illness or substance abuse, 
deemed by the Investigator to be likely to interfere with the 
interpretation of the results or which would interfere with a 
subject’s ability to sign or the legal guardian’s ability to sign the 
informed consent, and subject’s ability to cooperate and 
participate in the study  
 
Additional criteria: 
Subjects willing to participate in the correlative biologic studies will 
sign an additional consent form to provide additional tumor tissue. 
 

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ESTIMATED NUMBER OF 
PATIENTS/GEOGRAPHIC 
REGIONS 
200 evaluable (220 total) relapsed/refractory pediatric cancer patients. 
Additional patients may enroll through compassionate access if no 
other treatment options are available. 
 
Patients will enroll at: 
Arnold Palmer Children’s Hospital, FL   
St. Louis University/Cardinal Glennon Children's Medical Center, MO 
Helen DeVos Children’s Hospital, MI 
Levine Children’s Hospital, NC 
 
Connecticut Children's Medical Center, CT 
Children’s Mercy Hospital, Kansas City MO 
Rady Children’s Hospital of San Diego, CA 
Medical University of South Carolina, SC 
Monroe Carrell Jr. Children’s Hospital at Vanderbilt, TN 
Kapiolani Medical Center for Women and Children, HI 
Dell Children’s Hospital,TX 
Texas Children’s Hospital, Baylor College of Medicine,TX 
Primary Children’s Hospital, UT 
Children's Hospital and Clinics of Minnesota, MN  
Penn State Milton S. Hershey Medical Center and Children’s Hospital, 
Hershey, PA 
Arkansas Children’s Hospital – Little Rock, AR 
International Sites 
American University of Beirut Medical Center, Lebanon 
La Timone; Marseille, France 
 
 
LENGTH OF STUDY 
Accrual to this study is estimated to be approximately 3-4 years. 
 
STUDY ASSESSMENTS 
Refer to Table of Assessments for timing of study procedures. 
 
CRITERIA FOR 
EVALUATION 
Feasibility Measures: Primary objective:                                             
The definition of feasibility for this study will include: “Enrollment 
onto study, genomic profile, analysis and report generation 
completed, tumor board held with treatment decision, treatment 
review completed, start of treatment, and completion of 1 cycle of 
therapy.” 
 Efficacy Measures: Secondary objectives 
Response: 
To determine the overall response rate (ORR) by the presence of 
radiologically assessable disease by cross-sectional CT or MRI 
imaging and/or by MIBG or PET scans.  
 Duration of response, defined as the period of time from when 
measurement criteria are met for complete response (CR) or 
partial response (PR), whichever is first recorded, until the first 
date that recurrent or progressive disease (PD) is objectively 
documented (taking as reference for PD the smallest 
measurements recorded since the treatment started) 
 The assessment of response will include the initial measurable 

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targets and will be performed after cycle 2, then after every other 
cycle.  
 
 
• A subject will be defined as a responder if CR/PR is observed at 
any time of the treatment  
 
• Clinical response will be seen if stable disease and decrease in 
tumor markers by ≥ 50% or CR of bone marrow.  
 
• Time to progression, defined as the period from the start of the 
treatment until the criteria for progression are met taking as 
reference the screening measurements 
 
• Comparisons of ORR and PFS for the first and second cohorts of 
100 patients (i.e., those who enroll prior to versus after the 
implementation of Amendment 3.0, respectively) will be 
performed. 
 
Safety Measures: Secondary objectives 
• Safety analysis will be conducted on all subjects who have received 
at least one dose of therapy, and will include the frequency of all 
reported adverse events and laboratory abnormalities as well as 
frequency of dose interruptions, dose reductions and treatment 
discontinuation. 
 
STATISTICS/SAMPLE SIZE 
ESTIMATE 
200 evaluable subjects 
 
Patients who enroll following implementation of Amendment 3.0 
(second cohort of 100 patients) will have their tumor biopsies analyzed 
using an updated Drug Prediction Report (Appendix III).  Overall 
Response Rate (ORR) and Progression Free Survival (PFS) for this 
group will be compared to those of the first 100 patients who received 
treatment based upon the original Drug Prediciton Report and 
Pharmacopeia Library. 
 

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TABLE OF PROCEDURES AND ASSESSMENTS 
 
Procedure 
Screening 
Cycle 1 
Day 1 
Cycle 1 
Day 8 
Cycle 1 
Day 15 
Cycle 1 
Day 22  
(if applicable) 
Subsequent 
Cycles 
Day 1 
Off Therapy/ 
30 Day 
Follow-up 
Informed consent 
X 
 
 
 
 
 
 
Demographics 
X 
 
 
 
 
 
 
Medical history 
X 
X 
X 
X 
X 
X 
 
Baseline Symptom 
Form 
X 
X 
 
 
 
 
 
Concurrent meds 
X 
X 
 
 
 
X 
X 
Physical exam 
X 
X 
X 
X 
X 
X 
X 
Vital signs 
X 
X 
X 
X 
X 
X 
X 
Height 
X 
X 
 
 
 
X 
 
Weight 
X 
X 
 
 
 
X 
X 
Karnofsky or 
Lansky play score 
X 
X 
 
X 
 
X 
X 
CBC w/diff,  
X 
X 
X 
X 
X 
X 
X 
Serum chemistry * 
X 
X 
 
X 
 
X 
X 
Tumor Markers ** 
X 
X 
 
 
 
X 
X 
Adverse events 
 
 
X 
X 
X 
X 
X 
Surgical resection 
&/or diagnostic 
biopsy 
X 
 
MRI or CT*** 
X 
Radiologic measurements will be performed every 8 weeks or every 
other cycle (whichever occurs first) through Cycle 6, after which 
they may be performed as per institutional standard.  
MIBG/PET *** 
X 
Bone Marrow (any 
subject suspected to 
have BM disease ) ^ 
X 
Should be repeated every 8 weeks or every other cycle (whichever 
occurs first) only if positive at study entry; after Cycle 6, may be 
performed as per institutional standard. 
B-HCG 
X 
  
  
  
  
  
  
EKG (as indicated) 
 
 X 
  
  
  
  
  
* Serum electrolytes, BUN, Creatinine, Bilirubin, ALT, AST 
**LDH and/or Specific Tumor Markers for defined disease (if available) 
***Type of scan as indicated for disease type 
^Standard of Care Bone Marrow 
 
 
 
 
 
 
 
 
 
 
 
 

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1 
Background 
 
1.1 
Study Disease 
 
Relapsed or refractory neuroblastoma, brain tumors, and rare childhood tumors. 
 
1.2 
Rationale 
 
Lethality of Relapsed/Refractory Pediatric Cancers is an Unmet Clinical Need. 
 
Although improvements in the past 40 years have led to markedly improved survival rates of 
approximately 80% overall for pediatric cancers, patients with relapsed, rare and advanced stage 
tumors still have a very poor prognosis. Soft tissue sarcomas account for ~ 7% of pediatric 
cancers, with 850-900 new cases annually in the United States [1].  Rhabdomyosarcoma, the most 
common soft tissue sarcoma in children and adolescents, affects nearly 350 children in the United 
States each year [1].  Patients with metastatic rhabdomyosarcoma have a poor prognosis with an 
overall survival rate of ~30% [2]. The non-rhabdomyosarcoma soft tissue sarcomas affect ~500 
children each year.  Patients with metastatic non-rhabdomyosarcoma soft tissue sarcomas have 
long-term survival < 20% [3].  Malignant bone tumors (mainly Ewing’s Sarcoma and 
Osteosarcoma) account for 6% of childhood cancers, with ~400 cases of osteosarcoma and 200 
cases of Ewing’s Sarcoma diagnosed annually [1]. Patients with localized osteosarcoma, who 
have a poor response to pre-operative chemotherapy have a survival rate of around 50%, while 
patients with metastatic osteosarcoma or Ewing’s sarcoma disease at presentation, have a survival 
of < 20% [4, 5].  Renal cancers account for ~6% of pediatric cancer diagnoses, with 95% of cases 
being Wilms Tumor, which has a very favorable prognosis [1].  However, rare and high risk renal 
tumors such as metastatic anaplastic Wilms tumor, clear cell sarcoma of the kidney, renal cell 
carcinoma, and malignant rhabdoid tumor have an inferior outcome, with survival of < 20% [6, 
7]. For all these patients survival remains poor, despite use of dose-intensified multi-agent 
chemotherapy and stem cell transplantation. Therefore, new approaches such as targeted therapies 
are warranted. 
 
Neuroblastoma is the most common extracranial solid tumor in children, with approximately 700 
new diagnoses per year. It accounts for 7% to 10% of childhood cancers [8, 9].  Whereas the 
prognosis for infants with neuroblastoma is generally good, currently only 30% of children 
diagnosed after 12-15 months of age survive despite aggressive multimodal therapies [10, 11].  
Even with high-dose chemotherapy (HDC) followed by hematopoietic stem cell transplantation 
(HSCT) and maintenance therapy with retinoic acid the 5-year event-free survival remains below 
50% [12, 13].  Long-term survival of patients who are treated with conventional therapies 
following relapse is <5%. As such, neuroblastoma accounts for 15% of all pediatric cancer deaths 
in the United States [14]. Consequently, the evaluation of new drugs is strongly needed in this 
disease.  
 
Recent evidence has established the genetic heterogeneity of neuroblastoma and revealed the 
existence of several major molecular subsets that collectively may provide prognostic value for 
future disease management [15] [16]. While the poor prognosis for older neuroblastoma patients 
underscores the need for new treatment strategies, the elucidation of specific biologic subsets of 
neuroblastoma suggests a way to improve disease management. The current standard-of-care 

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treatments for relapsed neuroblastoma include a variety of Phase II or Phase I studies that 
generally have only modest response rates (10%-35%) [11]. Even in responding patients, tumors 
often go on to further rapid relapses and novel strategies to treat this patient population are 
urgently needed. There are currently few treatment options from which pediatric oncologists can 
select with any degree of confidence to improve the management of multiply recurrent 
neuroblastoma patients. The current strategy is to add salvage therapies based on the anecdotal 
experience of the treating physician, which often leads to drug-related toxicity but may or may 
not extend life. The identification of agents that target specific molecular pathways associated 
with the development and/or progression of neoplastic diseases holds promise. Improved 
approaches that identify in a more rational (data-driven) fashion combinations of existing agents 
that are likely to be effective should result in a survival benefit in the clinical setting, while 
avoiding the toxicity associated with agents that are unlikely to be beneficial. [17]. 
 
CNS tumors are the most common solid tumors in children, with 3000-4000 new diagnoses each 
year. CNS tumors account for approximately 25-30% of all childhood cancers. Though many of 
these CNS tumors are quite treatable, the 5-year survival for pediatric CNS tumors is only 
71%[18]. Patients who have relapsed and refractory CNS tumors are those most likely to 
succumb to their disease, in spite of aggressive chemotherapy and radiation, often followed by 
HSCT[19, 20]. Therefore, new treatment strategies are needed for control of CNS tumors. 
 
There is a growing focus on treating CNS tumors based on the biology of the disease[21, 22] 
rather than with “one size fits all” therapy. Risk stratification in CNS tumors based on biology is 
increasingly understood to be a priority. For example, medulloblastoma has been broken into 4 
biologic categories with different genetic mutations and different clinical outcomes[23-25]. 
Similar to neuroblastoma, these differences in the biology and clinical outcome of patients with 
medulloblastoma suggest new strategies to improve disease management. Ongoing clinical trials 
of upfront therapy for medulloblastoma are attempting to incorporate molecularly guided 
therapies. The current standard-of-care treatments for relapsed CNS tumors include Phase I and 
Phase II therapies that often have few, if any, responding patients[26, 27]. Again reflecting the 
challenges in neuroblastoma, responding patients with high grade CNS tumors often experience 
multiple relapses and are in dire need of novel treatment strategies. Improved approaches that can 
inform treatment regimens based on the biology of the disease could result in a survival benefit in 
this challenging patient population. 
 
Molecular Networks as the Drug Target.  
It is now firmly established that cancer results from perturbations in the molecular networks 
within cellular systems that disturb the normal homeostatic state [28-30]. Fluctuations in these 
networks can result from genetic or epigenetic cellular events and/or changes in the molecular 
constitution of the tumor microenvironment, which collectively dictate the phenotype of the 
biological system. The molecular networks engaged during tumor development and/or 
progression are complex. Molecular networks have evolved to provide the ultimate level of 
cellular plasticity, allowing cells to adapt to or exploit extracellular cues within the local milieu 
[31]. The complexity of a tumor system is further exaggerated by the inherent genomic instability 
seen in many neoplasms, which leads to an accelerated micro-evolutionary process that results in 
further cellular and tumor sub-system heterogeneity [32, 33]. This variability combined with the 
adaptability of many molecular pathways provides a somewhat predictable and highly probable 
path to resistance for any given agent that targets a subset of cellular systems within a tumor’s 
molecular and genetic repertoire [34]. A fundamental challenge in the area of targeted cancer 
treatment is how to identify optimal therapeutic combinations that can treat heterogeneous tumors 
that are both highly adaptive and that exhibit significant inter- and intra-patient variation [28, 35-
37]. Our proposal outlines an approach by which we can utilize our expanding knowledge of 
molecular networks and the mechanisms of action of a growing pharmacopeia [38, 39] in 

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conjunction with standardized biomarker assessments to deliver targeted combinations of 
effective therapies to pediatric cancer patients. 
 
Practice and Promise of Biomarkers for Patient Treatment Planning. 
A panel of individual biomarkers has recently been identified that can be used in the clinical 
setting to identify neuroblastoma patients most likely to respond to a specific therapy. For 
example, activation of the ALK gene through sequence variation mutations has been identified in 
a subset of neuroblastoma patients, and small-molecule inhibition of the ALK-encoded receptor 
tyrosine kinase caused cytotoxicity in affected neuroblastoma cell lines [40]. Such studies, in 
conjunction with a large body of in vitro and in vivo data, have further demonstrated that the 
efficacy of specific treatment modalities is dependent upon the molecular constitution of the 
tumor, and that the observed variations in tumor response to current therapies is attributable in 
large part to disease heterogeneity at the molecular level.  
 
While individual biomarkers may be predictive of responses to specific therapies, especially in 
the context of front-line treatment, a different approach to the management of patients with 
refractory disease is needed in order to identify effective treatments from the catalog of available 
agents. Advances in informatics and molecular technologies, coupled with our expanding 
knowledge of molecular networks and mechanism of action of the existing pharmacopeia, 
provide a great opportunity in translational medicine to develop a model that more accurately 
predicts tumor response. The studies outlined in this proposal are a step in the development of 
personalized oncology, in which each patient is truly treated individually based upon the 
systematic molecular analysis of their disease. Our project is focused on testing the merits of a 
specific data-driven predictive method through which any number of drugs in our current 
knowledge base has a chance of being recommended, of these only the FDA approved drugs 
listed in Appendix III will be used. Although this novel approach to personalized therapeutics 
brings with it to the concern that toxicities that may arise from novel combinations of agents, it is 
strongly felt by the investigators that the logical interpretation of molecular data by a committee 
of highly qualified physicians and pharmacists in order to identify drug candidates for 
consideration in the treatment of a patient population with few alternative options is a worthwhile 
endeavor. The systematic biomarker-driven approach outlined in this proposal, by tailoring a 
combination of drugs targeting the specific molecular composition of a tumor—irrespective of 
tumor classification or anatomical origin— provides a feasible alternative to the conventional 
approach that targets specific organs or tissues without consideration of the underlying tumor 
biology. 
 
 
A Pilot Trial Testing the Feasibility of using Molecular-Guided Therapy in Patients with 
Refractory or Recurrent Neuroblastoma. 
 
The primary objective of this pilot study was to evaluate the feasibility of using predictive 
modeling based on genome-wide mRNA expression profiles of neuroblastoma tumor biopsies to 
make real-time treatment decisions.  Feasibility was defined as the completion of the following in 
a two week time period: tumor biopsy, quality RNA extraction, mRNA U133 2+ Affymetrix gene 
chip hybridization, analysis utilizing a series of predictive methodologies, report generation, 
tumor board review with formulated treatment plan, and medical monitor review. Subjects were 
not treated on this study. There were 5 subjects enrolled between April-June 2010 with multiply 
relapsed or refractory neuroblastoma. Subjects had received between 2-13 previous relapsed 
therapies and were between 2-6.5 years post diagnosis. All subjects had soft tissue disease which 
was able to be biopsied. All biopsies were adequate by pathology evaluation (>75% viable tumor) 
and RNA quality (>6.5 RIN). Gene chips were completed in 3-7 days, report generation was 1-5 
days, tumor board was 1-3 days, medical monitor sign off was 1 day. The total time was 10-12 

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days for all subjects. The tumor board which consisted of 4-10 pediatric oncologists from sites 
across the US and a pediatric oncology pharmacist was able to create individualized therapy 
regimens for all subjects. Correlative biology specimens were obtained and grown in culture. 
Mice xenografts of 3/5 subjects were established. Cultures and xenografts are able to be used for 
validation studies of predicted drug sensitivity. In conclusion it is feasible to obtain real-time 
genomic profiling for molecularly guided therapy for use in treatment decision making.  
 
 
A Feasibility Trial using Molecular-Guided Therapy in Patients with Refractory or 
Recurrent Neuroblastoma. 
 
The primary objective of this feasibility study was to evaluate the feasibility and safety of using 
predictive modeling based on genome-wide mRNA expression profiles of neuroblastoma tumor 
biopsies to make real-time treatment decisions.  Feasibility was defined as “enrollment onto 
study, quality mRNA obtained, gene chip completed, tumor board held, medical monitor review 
and approval, start of treatment by 21 days post biopsy/surgical resection date, and completion of 
1 cycle of therapy.” Sixteen (16) subjects were enrolled to this study, all with multiply relapsed or 
refractory neuroblastoma. Subjects were between 1-11 years post diagnosis. All subjects had soft 
tissue disease which was able to be biopsied. All biopsies were adequate by pathology evaluation 
(>75% viable tumor) and RNA quality (>6.5 RIN). 2 subjects were deemed ineligible due to 
tumor type after biopsy. Gene chips were completed in 3-8 days (95% CI: 3.8 – 6.8), report 
generation took 0-3 days (95% CI: 0.0 – 1.5), tumor board took 1-6 days (95% CI: 1.6 – 4.2), 
medical monitor sign off took 1-2 days (95% CI: 0.8 – 1.4). The total time from date of biopsy to 
tumor board was 6-11 days (95% CI: 7.5 – 10.2) for all subjects and 7-20 days to treatment (95% 
CI: 8.9 – 16.1), with an average of 12.4 days. The tumor board which consisted of 4-15 pediatric 
oncologists from sites across the US and a pediatric oncology pharmacist was able to create 
individualized therapy regimens for all subjects. Correlative biology specimens were obtained 
and grown in culture. Mice xenograft establishment is ongoing. Cultures and xenografts are able 
to be used for validation studies of predicted drug sensitivity. Triplicate biopsies showed 
reproducible sets of drugs and the comparatively large differences in drug lists between patients 
show that the drug lists are tailored to patients. Comparison of RNA expression profiles with 
RNA sequencing from each patient showed strong correlation. 
 
The study endpoint showed that 14/14 patients were feasible to enroll, biopsy, genomic analysis, 
tumor board review and patient treatment was met. All regimens were found to be safe by the 
medical monitor proving that the molecular tumor board was able to make safe decisions similar 
to hospital tumor boards making treatment decisions without molecular information on the 
patients. It was felt that the pharmacy review for evaluating drug-drug interactions and deciding 
on laboratory and safety testing was an important part of the tumor board (this is not usually 
present at hospital tumor boards) and will continue to be incorporated in this and future trials.   
All patients tolerated therapy well and were treated without any serious adverse events related to 
study drugs. Clinical benefit was seen 64% of patients.  This study shows that it is feasible to 
create therapeutic treatment plans based on genomic profiling in real time and that patients are 
able to be treated safely on a tumor board derived molecular guided therapy using existing 
medications 
 
 
In this study we proposed to study reproducibility by applying it to triplicate samples obtained by 
dissecting each of five solid tumors. The primary goal of the reproducibility study is to evaluate 
the variation among sets of drug therapies associated with the same tumor. Secondary goals are 1) 
to compare the variation among sets of drug therapies from the same tumor with variation 

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between tumors from distinct patients and 2) to evaluate variation associated with earlier steps in 
the process, in particular, expression profiles and comparative expression profiles. 
   
 
 
Distance-based 
nonparametric 
multivariate 
analysis of variance [41, 42] allowed us to reject the null hypothesis that variation between 
biopsies can be accounted for by the variation within biopsies (p=0.001). That the variation 
among expression profiles associated with the same biopsy is small compared with the variation 
between expression profiles associated with different biopsies is apparent from Principal 
Component Analysis (Figure 1).  
 
Sets of drug therapies  
Similarly, the variation among drug sets associated with the same biopsy is small compared with 
the variation among drug lists associated with different biopsies (p=0.001). The reproducibility 
averaged over patients, replicates, and drugs is 0.68.  As the threshold score increases the 
reproducibility increases to 1 (Figure 2). 
 
A Feasibility Trial using Molecular-Guided Therapy in Patients with Relapsed and 
Refractory Childhood Cancer. 
 
The primary objective of this study was to determine feasibility of using tumor samples to assess 
genomic mRNA expression arrays and DNA Mutation Panels using predictive modeling to make 
real-time treatment decisions for children with relapsed/refractory cancers.  Feasibility was 
defined as “enrollment onto study, RNA expression profile completed, DNA Mutation Panel 
completed, genomic analysis and report generation, tumor board held with treatment decision, 
treatment review completed and start of treatment by 21 days post biopsy/surgical resection date, 
 
Figure 1 Principal Component Analysis. The first 
three principal component scores, PC1-PC3, 
illustrate the observation that the variation 
associated with the six samples for each biopsy 
(all of which have the same symbol and color) is 
small relative to the variation between biopsies.  
 
Figure 2. Reproducibility as a function of the 
threshold score. The reproducibility averaged 
over patients, replicates, and drugs is 0.68 (the 
intercept with the horizontal axis).  As the 
threshold score increases the reproducibility 
increases to 1. 

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and then completion of 1 cycle of therapy.” This study has completed accrual and final results 
will be reported at a future time point. 
 
Conclusion 
Collectively, the early preclinical and current clinical data suggests that this integrated approach 
is highly feasible and safe in pediatric cancers and that it is reproducible among repeat samples 
within patients. Based upon the significant need for a more rational-based approach to therapeutic 
selection in these difficult to treat pediatric tumors continued development of this approach is 
warranted. The area of genomic analysis is advancing rapidly and recently DNA exomes and 
RNA sequencing are now available by CLIA certified laboratories. We have adapted our analysis 
to move from RNA expression profiling to RNA sequencing and DNA mutation panel to DNA 
exomes. This will be evaluated in this study for use by the molecular tumor board in treatment 
decision making.   
2 
STUDY OBJECTIVES 
2.1 
Primary Objectives 
 
Determine feasibility of using tumor samples to assess genomic sequencing using predictive 
modeling to make real-time treatment decisions for children with relapsed/refractory cancers. 
 
2.2 
Secondary Objectives 
 
♦ To determine the activity of treatments chosen based on: 
• 
Overall response rate (ORR)  
• 
Progression free survival (PFS)  
♦ To continue to evaluate the safety of allowing a molecular tumor board to determine 
individualized treatment plans 
♦ (Voluntary) To explore the relationship between tumor phenotype/genotype and response 
by permitting use of tumor tissue in a correlative biologic study 
♦ To compare PFS interval to PFS intervals of previous chemotherapy regimens since 
relapse for each subject. 
♦ Sub analysis examination of disease types. 
2.3 
Subject Enrollment and Sample Procurement and Data Processing 
Eligible subjects will be enrolled onto this study at each site following a registration process that 
includes receipt of a signed subject consent form and a copy of the required baseline laboratory 
tests. Subjects will undergo a scheduled surgical resection and/or diagnostic biopsy procedure. 
Common sample identifiers will be provided by the NMTRC Lead Study Coordinator to the 
participating site and will be used by all parties throughout the project to ensure sample, data and 
report alignment between participating organizations.  At the time of tissue resection or biopsy, 
fresh tumor samples and a blood sample will be committed for this specific research study 
(referred to as “Primary Samples”), and prepared immediately per Appendix II and section 9.3. 
Primary Samples will be sent to Ashion Analytics, LLC, which is a CLIA-certified laboratory 
housed at the Translational Genomics Reserach Institute (TGen). Samples will be reviewed by 
local pathology to confirm that the sample sent to TGen contains >50% tumor  cell viability 
which is the minimum required for successful analysis. The absence of an adequate tumor 
specimen from an enrolled subject will make them not eligible to continue on the study.  Tumor 

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samples will also be sent for research purposes (referred to as “Secondary Samples.”) A portion 
of the tumor tissue biopsy will be shipped overnight to the Sholler Pediatric Oncology 
Translational Research Laboratory on dry ice.  
 
Upon arrival of the tumor specimens at Ashion and the Sholler Pediatric Oncology Translational 
Research Laboratory, the samples will be logged and immediately processed according to details 
in Section 9. 
2.4 
DNA and RNA Sequencing 
 
Sequencing for this study will be performed at Ashion Analytics, LLC (Ashion).  Ashion is a 
CLIA-certified laboratory developed by TGen in order to perform whole exome and RNA 
sequencing in a clinical laboratory to ensure the accuracy, reliability, and quality of the data. The 
sequencing will be performed on the Illumina HiSeq 2500 Sequencer. Quality thresholds will 
include metrics such as base calling quality, coverage, allelic read percentages, strand bias, and 
alignment quality. Once data has passed all QC thresholds, the de-identified data will be 
preprocessed and uploaded directly to the NMTRC TransMed software for creation of the 
NMTRC Drug Prediction Report. 
 
Data Flow 
At enrollment in the study, a patient record will be created and the tumor and blood samples for 
the patient will be given a sample identifier and stored in the NMTRC laboratory management 
database (LIMS). The samples, tagged with the LIMS sample identifier, will then be sent to the 
CLIA laboratory in Phoenix, AZ.  Once there, whole exome sequencing and RNA sequencing 
will be performed on the tumor sample. Whole exome sequencing will also be performed on a 
blood sample from the patient. For exome sequencing, fastq files are aligned with BWA 0.6.2 to 
GRCh37.62 and the SAM output are converted to a sorted BAM file using samtools 0.1.18. BAM 
files are subjected to indel realignment, mark duplicates, and recalibration steps in this order with 
GATK 2.2 where dpsnp135 is used for known SNPs and 1000 Genomes’ 
ALL.wgs.low_coverage_vqsr.20101123 is used for known indels. Lane level sample BAMs are 
then merged with Picard 1.79 if they are sequenced across multiple lanes. Variant calling is done 
with Unified Genotyper and the output VCF files are recalibrated with VariantRecalibrator from 
GATK 2.2. SnpEff 3.0, and SnpSift 1.7 is then used to annotate these VCF files with database 
version GRCh37.66.For RNA sequencing, lane level fastq files are appended together if they are 
across multiple lanes. These fastq files are then aligned with TopHat 2.0.6 to GRCh37.62 using 
ensembl.63.genes.gtf as GTF file and the resulting BAM files are assembled with Cufflinks 2.0.2 
using the same GTF file and ensembl.63.genes.MASK.gtf as the mask file. HTSeq 0.5.3 is used 
to count the number of reads spanning each gene. Changes in transcript expression are calculated 
with Cuffdiff 2.0.2. For novel fusion discovery, reads were trimmed to 50 base pairs and then 
aligned with TopHat-Fusion 2.0.6. At the completion of RNA Sequencing, two files will be 
produced that will be consumed by the personalized medicine reporting engine. The first of these 
files is a VCF file that specifies the variants that were observed in the tumor sample. The second 
file is an FPKM file that specifies the expression levels of genes in the tumor sample. Both of 
these files will be in the VCF 4.1 format - an example of the VCF 4.1 format for expression is 
shown in the appendix.  At the completion of the whole exome sequencing, a single file VCF file 
containing the variants for the tumor sample and identifying them as either somatic or germ line 
by comparison to the normal blood sequence. The tumor variants will be in VCF4.1 spec 
generated by Seurat 2.5.  An example of a variant (for the V600E mutation of BRAF) is shown in 
the appendix below where AR is allele ratio, DP1 is depth of normal, DP2 is depth of tumor, LN1 
is length.  The effect of the variant is extracted with the following regular expressions, regex is 
EFF=/\((.*)\)/.  

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Patient data captured on the Ashion server is encrypted and pushed via a file transfer server (FTP) 
for secure delivery of data to authorized NMTRC study personnel. The LIMS system contains a 
file detection system that will identify when samples are made available on the FTP site. These 
files, tagged with the sample identifiers will be pulled from the FTP site and imported into the 
LIMS system. The LIMS system will then process the three files into a personalized medicine 
report as described in the algorithms section. 
 
2.5 
NMTRC Drug prediction report 
 
The following describes the NMTRC report generation which utilizes data generated from 
Ashion (as described in section 2.4 above). 
 
 
Predicted Therapeutic Compounds:  At this time, there are currently greater than 200 drugs 
within the NMTRC drug library each with previously defined or inferred molecular targets.  For 
the purposes of this protocol, the tumor board will only use the drugs listed in Appendix III. 
 
Algorithms    
 
There will be three drug matching algorithms utilized in this molecularly guided therapy protocol.  
 
1. Direct variant/drug matching 
2. Inferred variant/drug matching 
3. Expression of biomarkers/drug targets (biomarker expression) 
The algorithms are described in detail below. Although there will not be formal ranking of the 
drug calls, there are different levels of confidence in the three algorithms and as such, the drugs 
will be listed in the report in the order of the confidence in the algorithms that identified them as 
candidate therapies for the patient (Direct variant first, followed by inferred variants, followed by 
biomarker expression). This is because sequence variants (whether direct or inferred) provide 
stronger evidence of tumor dependence than simple gene expression calls, with direct 
drug/variant relationships being the highest confidence of all three.  Within the biomarker 
expression, the drugs will be listed in descending order from most to least differentially 
expressed. 
 
Variant drug matching 
 
The NMTRC LIMS system has a database that contains a table linking drugs, variants, and genes 
with evidence from peer reviewed literature. The patient's tumor variants from the VCF files 
produced by Ashion are linked to the variants and genes in this table to identify potential 
therapies. This matching provides the output for direct variant/drug matching and inferred variant 
drug/matching. The inferred and direct refer to the strength of the evidence supporting the 
relationship between the drug and the variant. The first level of confidence, direct evidence 
indicates that the literature indicates that 1) the variant has been directly associated with a change 
in response to the therapy (either becoming more sensitive or more resistant) and the gene is the 
target of the drug or 2) the variant has been directly shown to activate the pathway for which the 
drug is a target or 3) the variant has been associated with changes in response to the drug due to 
indirect mechanism including but not limited to transportation or metabolism. Evidence of direct 
activation of the drug target by the variant is considered a sensitivity indicator, unless there is 
specific evidence that the variant induces resistance to the drug. The second level of confidence, 

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inferred evidence, indicates that the variant is in a gene that is a direct target of a drug and is 
computationally predicted to have biological impact in the gene, but the variant has not been 
directly associated with changes in response to drug or activation of target.  For inferred variants 
the variant must be a somatic mutation (present in the tumor only) and also have a minor allele 
frequence from the 1000 genomes project which is less than 0.5%.Whether the evidence is direct 
or inferred will be indicated by a column in the report. The evidence that resulted in the drug 
selection will be provided as a hyperlink in the table. 
 
Biomarker Expression 
 
The third algorithm utilizes the gene expression as measured by RNASeq. A consistent step for 
the NMTRC methodologies outlined in this proposal is the conversion of normalized probe set 
intensities to a relative measure of transcript abundance.  We utilize a standardized z-score 
method (described below in Signal Pre-Preprocessing and Z-Score Calculation) to determine 
statistically significant differences in each sample relative to a whole body reference and relative 
to cancer reference.  This method assigns a z-score to each probe set based upon the number of 
standard deviations from the normal sample population mean.  This provides a good assessment 
of transcript “differences” relative to a whole body reference or cancer reference sets which may 
not necessarily be associated with large fold changes in transcript expression. Having established 
a consistent data input of relative transcript abundance in each subject’s tumor specimen, the 
following analytical methods will be applied to the standardized data to predict drug efficacy. 
 
The method is fundamentally very straightforward. There are two classes of expression rules. The 
first of these rules are biomarker rules and are of the type “overexpression of gene g1 implies 
sensitivity (or insensitivity) to drug d1” or “underexpression of gene g2 implies sensitivity (or 
insensitivity) to drug d2” whereas the second is “g3 is the target of drug d3, thus overexpression 
of g3 implies sensitivity to d3”. The NMTRC LIMS contains a database of drugs and the genes 
along with a column that implies whether over or under expression of that gene indicates 
sensitivity (or insensitivity) to the drug and the evidence for that rule. In order for a gene to be 
called over or underexpressed a method is required to identify calls. This is described in more 
detail in the next section. 
Gene expression calls 
 
Two distinct perspectives are consistent with using over- or underexpression to guide therapy but 
suggest different sets of reference samples and different statistical tests. If gene expression level 
is interpreted to reflect sensitivity of a cell to a drug then elevated (alternatively, depressed) 
expression should be anomalous by comparison with normal cells throughout the body (the whole 
body normal reference). The drug should then kill the tumor cells before it kills normal cells. We 
call elevated (depressed) expression relative to samples of the whole body Normal Reference 
using a standard score (Z-score), referred to as the NRZ.  
In contrast, if gene expression level in a cancer cell is interpreted as reflecting comparative drug 
sensitivity among cancer cells then elevated expression should be called based on its rank among 
other cancer samples (the cancer reference). We call elevated (alternatively, depressed) 
expression relative to the Cancer Reference based on the Cumulative distribution, referred to as 
the CRC statistic.  
We report indications based on both the NRZ and CRC, based on only the NRZ, and based on 
only the CRC. For each such indication we report both the NRZ and the CRC. 
 

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Normal Reference Z-score (NRZ) 
𝑁𝑁𝑁𝑁𝑁𝑁=
𝑋𝑋𝑞𝑞−𝑋𝑋ത𝑅𝑅
𝑠𝑠𝑅𝑅
 
where 𝑋𝑋 is the normalized expression of Anders and coworkers [43]. 𝑞𝑞 indicates the query 
(cancer) sample, 𝑋𝑋ത𝑅𝑅 is the reference sample mean of 𝑋𝑋, and 𝑠𝑠𝑅𝑅 is the reference sample standard 
deviation of 𝑋𝑋. The NRZ is consistent with the statistic we used previously for microarray-based 
expression measurements. We use a threshold of 2, that is, NRZ>2 indicates overexpression NRZ 
< -2 indicates underexpression. The normal reference set comprises 42 normal tissues, organized 
into 21 tissue types: Adrenal Gland, Brain, Bronchus, Corpus uteri, Corpus Uteri, Esophagus, 
Gland, Heart, Large Intestine, Liver, Lymph Node, Nipple, Prostate Gland, Salivary Gland, 
Skeletal Muscle, Skin, Small Intestine, Spleen, Testis, Tonsil, Uterus. Many (28) of the samples 
are also given a sub-type designation, for example, Brain: Hippocampus. 
Cancer Reference Cumulative statistic (CRC) 
𝐶𝐶𝐶𝐶𝐶𝐶= ൜𝐸𝐸𝑖𝑖∈𝐶𝐶[𝑍𝑍𝑖𝑖> 2]
Overexpression
𝐸𝐸𝑖𝑖∈𝐶𝐶[𝑍𝑍𝑖𝑖< −2]
Underexpression 
where 𝐸𝐸𝑖𝑖∈𝐶𝐶[ ] indicates an average over the set, 𝐶𝐶, of cancer cases, 𝑍𝑍𝑖𝑖=
𝑋𝑋𝑞𝑞−𝑋𝑋ത𝑖𝑖
𝑠𝑠𝐶𝐶 is the standard 
score for the query by comparison with cancer case 𝑖𝑖, 𝑋𝑋ത𝑖𝑖 is the mean associated with samples 
from case 𝑖𝑖 , and 𝑠𝑠𝐶𝐶 is the sample standard deviation, obtained from 𝐶𝐶. CRC estimates the 
proportion of cancer samples that are less extreme than the query, that is, a higher CRC indicates 
more strongly for treatment based on the rule. For example, with an overexpression rule, CRC = 1 
means that expression in the query sample was higher than in all cancer reference samples by at 
least 2 standard deviations. We have chosen to call samples that are in the top quartile 
(CRC>0.75) as elevated or depressed in expression. We also identify genes support by both NRZ 
and CRC when NRZ > 2 and CRC > 0.5. 
In contrast to the use of the use of the NRZ, with which the objective is to call anomalous 
expression, comparison with the cancer reference requires estimating the quantile associated with 
𝑋𝑋𝑞𝑞. The proportion of cancer samples that express a gene at a level below the query sample might 
be estimated using the empirical cumulative distribution function, for example, in the case of 
overexpression 
𝐸𝐸𝑖𝑖∈𝐶𝐶ൣ𝑋𝑋𝑞𝑞> 𝑋𝑋𝑖𝑖൧. 
However, variation arises as a result of biological differences between tumors and as a result of 
differences in observations of the same tumor. If all tumors were biologically identical with 
respect to expression of a gene then quantiles would reflect exclusively the observation and 
variation would not be relevant.   Since our cancer reference set includes samples representing 
pediatric oncology tumors we can estimate the variation within cancer case and therefore estimate 
the proportion of cancer cases for which expression of the gene falls significantly below 
(overexpression) or above (underexpression) the query. 
Report: 
The process of report generation begins when all of the sequencing data is available on the FTP 
server. If gene matches gene in the database then aberration is checked. For each gene/variant that 

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matches a rule in the rules database, a row will be generated in the report. All variants supported 
by direct evidence will be listed first in the report indicating their greater clinical significance and 
an indication that the relationship is supported by direct evidence. If an aberration meets the 
criteria for an inferred indicator of drug response (described in the algorithms section) it will 
generate a line in the report which indicates that the relationship between the drug and gene is 
inferred. For each differentially expressed biomarker indicating/not indicating, a line will 
be generated in the report. For all rows in the report there will be a link to the PubMed article that 
supports the identified aberration/drug relationship. The set of rules will be in a read only 
database that will be inaccessible for changes during the trial.  
The software has been validated to show that: 
1. 100% reproducible output given the same input.  
2. Simple yet sophisticated rules management.  
3. Cross reference data with several open source data sets. 
4. Generation of a clinically understandable, actionable report. 
Positive mutation findings from the whole exome and RNA sequencing will be verified using 
Sanger Sequencing. While all attempts will be made to have this data available to the tumor 
board, due to the potential length of time to process Sanger Sequencing samples, these results 
may not be available until after the tumor board has met and the patient has started protocol 
treatment. If Sanger Sequencing results differ from the original sequencing, the results and the 
subject has already started protocol treatment, this information will be communicated to the 
treating site Principal Investigator who will then communicate this information to the patient and 
a mutual decision about continued treatment will be made. 
3 
Treatment Protocol Decision 
3.1 
Decision Making Rules for Treatment Regimens 
Treatments protocols will be generated from the molecular tumor board meeting utilizing the 
information contained in a report generated on the basis of genomic analysis of the gene 
expression profile of the subject’s tumor. The molecular tumor board consists of pediatric 
oncologists, pharmacists, bioinformations, genomicists, and pathologists (as available).  Specific 
treatment details will consist of a regimen chosen from a guided list of agents implicated in 
critical molecular signaling pathways summarized in the guided therapy reports and may include 
one standard chemotherapy agent not included on the report. All agents are listed in the current 
FDA approved pharmacopoeia with age appropriate dosing, but will differ amongst individual 
subjects. 
3.1.1 Decision rules for the committee will include:  
1. All drugs with predicted efficacy will be reported to the tumor board. At this time, FDA 
approved and over the counter medications predicted by one of the different predictive 
methodologies under evaluation will be included. For these panels the analytical methods 
are independently applied to the standardized and normalized (relative to whole body and 
cancer reference sets) gene sequencing data derived from the profiling of each subject’s 
tumor. Each method is associated with an objective statistical threshold that must be 

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exceeded in order for a specific drug to be predicted and reported for consideration. 
Molecular-based predictions of drug efficacy will be supplemented with evidence 
gathered from searching of the literature, clinical trials and the internet.  
2. Drugs must be FDA approved or available over the counter with established standard and 
safe age appropriate dosing schedules.  
3. Potential drug choices will be analyzed with regards to safety, mechanism, availability 
and cost. Focus will be on low-toxicity, targeted therapies.  
4. Drug combinations will be allowed, up to a maximum of 4 agents. Literature searches 
will be conducted to assemble data on previously established and tested regimens. These 
regimens will be given priority. 
5.  A pharmacist will analyze potential drug interactions between the guided agents and the 
subject’s routine medications and supplements. For drug interactions and known 
toxicities the following databases will be used: MicroMedex LexiComp, Facts and 
Comparisons, Natural Medicines Database. 
Subjects’ history and previously received treatments will be reviewed. Drugs which a subject 
has failed will be given low priority and used only if there is a rationale for synergy in 
combination therapy. 
3.1.2 Recommended priorities for determining drug dosing to be used in individualized 
treatment plans include the following: 
1. For a given proposed individualized combination of drugs the first priority to establish 
doses will be to identify the same combination of drugs in a peer-reviewed journal article 
or presented as a reviewed abstract, or which is part of an ongoing peer-reviewed clinical 
trial registered with clinical trials.gov. 
2. When a proposed individualized combination of drugs has not previously been reported, 
the process to establish doses will be to then identify individual members of the proposed 
combination that have been used in combination with other cytotoxic agents similar to 
those being considered for combination therapy. The source of information will be a 
peer-reviewed journal article or presented as a reviewed abstract, or which is part of an 
ongoing peer-reviewed clinical trial registered with clinical trials.gov. 
3. When a proposed individualized combination of drugs have no available combination 
data, dosing guidelines will start with the MTD determined from a phase I/II pediatric 
study.  Reference information will be based upon either a peer-reviewed journal article or 
presented as a reviewed abstract, or which is part of an ongoing peer-reviewed clinical 
trial registered with clinical trials.gov.  Doses will be reduced to compensate for potential 
additive toxicities of combination agents.  
Please note that many of the drugs that will be considered for proposed individualized 
combination therapy in this protocol are not considered cytotoxic agents and therefore will not 
have previously been specifically tested as part of conventional antineoplastic protocols. 
Examples of these medications may include anti-seizure or anti-cholesterol agents. These non-
cytotoxic agents will be used at standard doses based on recommendations of an experienced 
pediatric pharmacist and described pharmacy programs that are used to evaluate potential 
interactions and combination dosing for all medications. The final treatment regimen will be 
subjected to a 12 hour in depth review and evaluation for safety and then be signed off by one of 
the protocol pharmacists. The treatment memo will then be discussed with the subject and their 
parents (if the subject is < 18 years of age). 
 

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3.2 
Additional Biopsies: 
 
Subjects that are having additional biopsies done as standard of care during the course of the 
study, when deemed appropriate by study PI, may complete the study process again and have new 
reports generated on the latest tumor. A new tumor board discussion will occur utilizing all rules 
of this protocol and the new reports. The subject may then change treatment regimens based on 
the decision of the tumor board. All protocol requirements and specifications will be followed as 
if it were a new biopsy. 
 
3.3 
Safety Evaluations 
The principal investigator and the study chairs will evaluate reported serious adverse events and 
other toxicities in real time.  Study chair and PI meetings will occur at least monthly. The 
principal investigator will meet with the clinical research team at frequent and regularly 
scheduled intervals to determine treatment modifications and treatment based toxicities.  
 
Any safety concern or new information that might affect either the safety or the ethical conduct of 
this trial will be immediately forwarded to the study chairs in written form.  The NMTRC will be 
responsible for informing the central IRB and DSMB.  If trends in toxicities are noted or stopping 
rules are met, the study chair will temporarily suspend enrollment while reviewing the episodes 
with the DSMB. The DSMB will convene every 6 months for evaluation of all safety data. 
 
Study will be on hold for safety monitoring by DSMB review when: 
1. Any deaths deemed related to the study drug by the treating PI while on study or 
occurring less than 30 days after medications ended or 2 serious adverse events 
possibly related to protocol within 60 days. 
2. Any other reason that the NMTRC feels it is in the best safety interest of the subjects.  
Subjects will be required to either come off study or be dose reduced per treating physician 
standard of care if one of the following toxicities related to treatment regimen occurs. Toxicity 
will be graded according to the NCI-Common Terminology Criteria for Adverse Events (CTCAE 
v4.0). 
 
 
Non-Hematologic toxicity: 
∙ ≥Grade 3 non-hematological toxicity not resolved to <Grade 2 or baseline 
within 2 weeks excluding nausea, vomiting, anorexia, hypertension, electrolyte 
abnormalities corrected with oral supplementation. 
 
 
 
Hematologic toxicity: 
∙ Grade 4 neutropenia lasting ≥14 days; 
 
∙ Grade 4 neutropenia with Grade 4 infection 
 
 

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3.4 
Efficacy Evaluations  
At the times indicated in Section 4 and the Table of Procedures and Assessments, scans will be 
obtained to evaluate response data for subjects enrolled in this study. Efficacy will be assessed 
according to criteria outlined in Section 6 (Efficacy Assessments) to evaluate the activity and 
potential benefit of the chosen treatments protocol in this subject population.  
 
3.5 
Biological Studies  
Subjects will have an opportunity to participate in correlative biological studies on a voluntary 
basis. This study will be used to correlate in vivo and in vitro predictive drug responses.  This 
study may be able to contribute to our knowledge of molecular determinants of response to 
therapy and/or development of biomarkers to help guide future therapy. 
 
 
3.6 
Treatment during waiting period 
Subjects will be allowed to receive one cycle of standard of care or treating physician chosen 
therapy after their biopsy and before starting tumor board defined therapy in order to prevent 
progression during this waiting period. Subjects that opt to have this cycle of therapy will need to 
have recovered from hematological effects (to baseline) and have repeat scans of their primary 
tumor sites and any sites being followed for study efficacy before starting tumor board defined 
therapy. 
 
4 
 SUBJECT SELECTION 
4.1 
Inclusion Criteria 
1. Subjects must have proven pediatric cancer with confirmation at diagnosis or at the time of 
recurrence/progression and clinical determination of disease for which there is no known 
effective curative therapy or disease that is refractory to established proven therapies fitting 
into one of the following categories: 
a. Neuroblastoma- Patients that have relapsed following standard of care therapy (such as 
high risk patients, patient presenting after age 15 months or MYCN amplified, and only 
following (for eligible patients) high-dose chemotherapy followed by hematopoietic 
stem cell transplantation and maintenance therapy with retinoic acid and antibody 
therapy) or having progressed during standard of care therapy and non-
responsive/progressive to accepted curative chemotherapy. 
b. Brain Tumors 
i. Medulloblastomas (At relapse after standard of care therapy [surgery, 
chemotherapy and/or radiation] and/or non-responsive/progressive on accepted 
curative therapy) 
ii. Gliomas (At relapse after standard of care therapy [surgery and/or radiation 
and/or chemotherapy] and/or non-responsive/progressive on accepted curative 
therapy) 
iii. Diffuse Intrinsic Pontine Glioma/DIPG/Diffuse Midline Tumor- (At diagnosis, 
as there is no known curative therapy) 
iv. Glioblastoma Multiforme- (At diagnosis, as there is no known curative therapy) 
v. Ependymomas (At relapse after standard of care therapy [surgery with or 
without radiation] and/or non-responsive/progressive on accepted curative 
therapy) 

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vi. Choroid plexus tumors (At relapse after standard of care therapy [surgery] 
and/or non-responsive/progressive on accepted curative therapy) 
vii. Craniopharyngiomas (At relapse after standard of care therapy [surgery or 
suppressive therapy] and/or non-responsive/progressive on accepted curative 
therapy) 
viii. Dysembryoplastic neuroepithelial tumors (DNETs) (At relapse after standard of 
care therapy [surgery] and/or non-responsive/progressive on accepted curative 
therapy) 
ix. Meningiomas (At relapse after standard of care therapy [surgery] and/or non-
responsive/progressive on accepted curative therapy) 
x. Primitive Neuroectodermal Tumors (PNETs)/CNS Embryonal Tumors (At 
relapse after standard of care therapy [surgery, chemotherapy, and/or radiation] 
and/or non-responsive/progressive on accepted curative therapy) 
xi. Germ cell tumors (At relapse after standard of care therapy [surgery, and/or 
radiation and/or chemotherapy] and/or non-responsive/progressive on accepted 
curative therapy) 
xii. Atypical Teratoid Rhabdoid Tumor (ATRT) (At relapse after standard of care 
therapy 
[surgery, 
chemotherapy 
and/or 
radiation] 
and/or 
non-
responsive/progressive on accepted curative therapy) 
c. Rare Tumors: 
i. Soft tissue sarcoma 
Rhabdomyosarcoma (At relapse after standard of care therapy [surgery, and/or 
radiation, chemotherapy] and/or non-responsive/progressive to accepted curative 
chemotherapy) 
Non-rhabdomyosarcoma (At relapse after standard of care therapy [surgery, 
and/or radiation, chemotherapy] and/or non-responsive/progressive to accepted 
curative chemotherapy) 
ii. Bone 
Ewings sarcoma (At relapse after standard of care therapy [surgery, and/or 
radiation, chemotherapy] and/or non- responsive/progressive to accepted 
curative chemotherapy) 
Osteosarcoma (At relapse after standard of care therapy [surgery, chemotherapy] 
and/or non- responsive/progressive to accepted curative chemotherapy) 
iii. Renal 
Wilms tumor (At relapse after standard of care therapy [surgery, and/or 
radiation, chemotherapy] and/or non- responsive/progressive to accepted 
chemotherapy) 
Renal cell carcinoma (At relapse after standard of care therapy [surgery, 
chemotherapy] and/or non- responsive/progressive to accepted curative 
chemotherapy) 
Malignant rhabdoid tumor (At diagnosis, as there is no known curative therapy) 
Clear Cell Sarcoma- (At relapse after standard of care therapy [radiation, 
chemotherapy] and/or non- responsive/progressive to accepted curative 
chemotherapy) 
iv. Germ Cell tumors (At relapse after standard of care therapy [surgery, 
chemotherapy] 
and/or 
non-responsive/progressive 
to 
accepted 
curative 
chemotherapy) 

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v. Liver Tumors (At relapse after standard of care therapy [surgery, chemotherapy] 
and/or non- responsive/progressive to accepted curative chemotherapy) 
vi. Carcinomas- (At relapse after standard of care therapy and/or non- 
responsive/progressive to accepted curative chemotherapy)   
vii. Desmoid tumors- (At relapse after standard of care therapy and/or non- 
responsive/progressive to accepted curative chemotherapy)   
viii. Malignant Peripheral Nerve Sheath Tumors (MPNST)- (At diagnosis, as there is 
no known curative therapy) 
ix. Pheochromocytoma (At relapse after standard of care therapy and/or non- 
responsive/progressive to accepted curative chemotherapy).   
x. Ethesioneuroblastoma (At relapse after standard of care therapy and/or non- 
responsive/progressive to accepted curative chemotherapy). 
xi. Neuroendocrine tumors (At relapse after standard of care therapy and/or non- 
responsive/progressive to accepted curative chemotherapy). 
xii. Desmoplastic small round cell tumor (At relapse after standard of care therapy 
and/or non- responsive/progressive to accepted curative chemotherapy). 
xiii. Melanoma (At relapse after standard of care therapy and/or non- 
responsive/progressive to accepted curative chemotherapy). 
2. Subjects must be age >12 months at enrollment 
3. Subjects must be age  ≤ 21 years at initial diagnosis  
4. Subjects must have measurable disease as defined by RESIST v1.1   at the time of biopsy 
and tumor must be accessible for biopsy. Tumor samples submitted for analysis must contain 
>50% viable tumor tissue to qualify. In addition, subjects with disease confined to the bone 
marrow  are eligible to enroll if the degree of marrow involvement is expected to be >50%. 
Note: Subjects who are expected to have no evidence of disease after surgical removal of 
their tumor are still eligible for this trial if their disease would normally require adjuvant 
chemotherapy treatment after surgery despite NED status.  
5. Current disease state must be one for which there is currently no known effective therapy   
6. Specimens will be obtained only in a non-significant risk manner and not solely for the 
purpose of investigational testing. 
7. Lansky or Karnofsky Score must be ≥ 50 
8. Subjects without bone marrow metastases must have an ANC > 750/μl to begin treatment. 
9. Subjects with CNS disease currently taking steroids must have been on a stable dose of 
steroids for 2 weeks prior to their biopsy and must not have progressive hydrocephalus at 
enrollment.  
10. Adequate liver function must be demonstrated, defined as: 
a. Total bilirubin ≤ 1.5 x upper limit of normal (ULN) for age AND 
b.  ALT (SGPT) < 10 x upper limit of normal (ULN) for age 
11. A negative serum pregnancy test is required for female participants of child bearing potential 
(≥13 years of age or after onset of menses) 
12. Both male and female post-pubertal study subjects need to agree to use one of the more 
effective birth control methods during treatment and for six months after treatment is 
stopped. These methods include total abstinence (no sex), oral contraceptives (“the pill”), an 
intrauterine device (IUD), levonorgestrol implants (Norplant), or medroxyprogesterone 
acetate injections (Depo-provera shots). If one of these cannot be used, contraceptive foam 
with a condom is recommended. 

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13. Informed Consent: All subjects and/or legal guardians must sign informed written consent. 
Assent, when appropriate, will be obtained according to institutional guidelines 
4.2 
Exclusion Criteria 
1. Subjects who have received any cytotoxic chemotherapy within the last 7 days prior to 
biopsy  
2. Subjects who have received any radiotherapy to the primary sample site within the last 14 
days (radiation may be included in treatment decision after biopsy). 
3. Subjects receiving any investigational drug concurrently. 
4. Subjects with uncontrolled serious infections or a life-threatening illness (unrelated to tumor) 
5. Subjects with any other medical condition, including malabsorption syndromes, mental 
illness or substance abuse, deemed by the Investigator to be likely to interfere with the 
interpretation of the results or which would interfere with a subject’s ability to sign or the 
legal guardian’s ability to sign the informed consent, and subject’s ability to cooperate and 
participate in the study  
 
Additional criteria: 
Subjects willing to participate in the correlative biologic studies will sign an additional consent 
form to provide additional tumor tissue. 
 
5 
STUDY PROCEDURES AND ASSESSMENTS  
5.1 
Enrollment of Subjects  
 
All subjects (or subjects’ legal representatives) must provide written informed consent before any 
study specific assessments may be performed. The NMTRC will keep a “possible enrollment list” 
for all sites combined. Subjects will be allowed to enroll in the order that they are added to that 
list. Prior to consent of the subject, the NMTRC research coordinator will be contacted (via e-
mail) to place subject on this possible enrollment list. The NMTRC coordinator will then reply 
with study space availability. If a spot is not available at that time, the site will be contacted as 
soon as a spot does open up (based on the subject’s order on the list). If a spot is available at the 
time, the potential subject will undergo consent and completion of all required screening 
procedures and certification of all inclusion and exclusion criteria by the Investigator. If the 
subject fits all enrollment criteria, the site will again contact the coordinator at the NMTRC for 
official enrollment confirmation and unique subject identifier assignment. In addition, a study 
enrollment form will be e-mailed or faxed to the coordinator at the NMTRC. A subject may NOT 
be enrolled on trial until official approval from the NMTRC is received. When a spot becomes 
available, the first subject from the list will be contacted and will have 5 working days with which 
to enroll in the study. If this subject does not enroll by that time then the subject forfeits his/her 
spot and the next subject will be offered that spot.  
 
 
 

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5.2 
Screening  
The Investigator is responsible for keeping a record of all subjects screened for entry into the 
study and subsequently excluded.  
 
The following screening procedures must be performed within 21 days (14 days preferred) 
prior to date of biopsy*.  Studies must be done after last previous treatment for malignancy: 
  
1. Signed informed consent form. All subjects (or subjects’ legal representatives) must 
provide written informed consent before any study specific assessments may be 
performed. Signed informed consent form for voluntary participation in correlative 
biologic analysis;  
2. Complete medical and surgical history, including documentation of the evidence of 
malignancy and prior treatments for cancer. Include all other pertinent medical conditions 
and a careful history of all prior medical treatments;  
3. Demographics;  
4. Physical examination (including height and weight), noting all abnormalities and sites of 
palpable neoplastic disease;  
5. Vital signs, including temperature, pulse rate, and blood pressure;  
6. Karnofsky Performance status/Lansky Play status (Appendix I); 
7. Complete Screening Baseline Symptom form; 
8. CBC with differential; 
9. Serum electrolytes (sodium, potassium, chloride, bicarbonate), blood urea nitrogen 
(BUN), creatinine, albumin, Bilirubin, ALT, and AST; 
10. LDH and/or Specific Tumor Markers for defined disease (if available); 
11. Serum pregnancy test for female subjects of child bearing potential (onset of menses or 
≥13 years of age); 
12. CT or MRI of measurable disease sites (as indicated for tumor type); 
13. Solid tumor biopsy for “Primary Sample” with remaining tumor tissue used in correlative 
biologic studies handled per section 9.3 and submitted per Appendix II.  
For subjects that cannot provide a solid tumor biopsy; a bone marrow core biopsy sample 
will replace the solid tumor sample as the “Primary Sample.” Bone Marrow must have 
adequate tumor (defined as >50% tumor) in order to qualify as “Primary Sample.”  
 
*NOTE: If standard-of-care sample collection occurred within 12 weeks prior to 
enrollment and after last previous treatment for malignancy, and frozen sample 
remains, a subject may enroll using previously collected samples. Samples must 
additionally have been snap frozen within 20 minutes of collection and kept in a          
-70/-80 freezer.  
 
14. Concomitant medications/therapies including documentation of steroid use and dose; 
15. Confirmation of inclusion and exclusion requirements. 
 
Following completion of all required screening procedures and certification of all inclusion and 
exclusion criteria by the Investigator, the coordinator at the NMTRC will be contacted (via e-mail 
or phone call), at which time the subject will be enrolled in the trial and a unique subject number 
assigned.  
 
 

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The following screening procedures must be done prior to the first dose of study drug, but 
are not required to be done before biopsy.  
1. MIBG/PET scan (if indicated for tumor type). Other imaging appropriate for tumor type 
may also be considered. 
2. Any subject that is suspected to have possible bone marrow disease: Bone marrow 
aspirate and biopsy.  
3. Completion (by study staff) of pre-study case report forms. 
4. Any additional labs or testing required by the tumor board. 
 
 
For subjects that receive one cycle of treatment while waiting to start tumor board defined 
treatment (per section 2.11) or if patient did not receive treatment but more than 28 days 
since last assessment has occurred prior to starting study treatment: The following 
additional screening procedures must be performed AFTER the last dose of this additional 
cycle of therapy and PRIOR to the first dose of tumor board defined treatment:  
1. Repeat CT or MRI of primary disease sites and any disease sites being followed for study 
endpoints.  
2. CBC with differential- subject must be hematologically recovered to baseline before 
starting tumor board defined treatment. 
 
5.3 
Study Procedures/Study Interventions 
 
5.3.1 Study Visits- Cycle 1 Day 1 (may have been done within 5 days of treatment start/day 1,  
unless otherwise indicated as “same day”) 
Subjects will return to the enrolling clinic at Day 1 of cycle 1 for evaluations.  The following 
evaluations will be conducted prior to starting study drug: 
1. Physical examination (including body weight) and medical history (same day); 
2. Karnofsky Performance status/Lansky Play status-Appendix I (same day); 
3. Vital signs, including height, weight, temperature, pulse rate, and sitting blood pressure  
(same day); 
4. CBC with differential; 
5. Serum electrolytes, BUN, creatinine, Bilirubin, ALT, AST; 
6. LDH and/or Specific Tumor Markers for defined disease (if available);  
7. Baseline EKG (as indicated); 
8. Cycle 1 Day 1 Baseline Symptom Form (same day); 
9. Review and recording of concomitant medications (same day); 
10. Completion (by study staff) of Case Report Forms; 
11. Any additional labs or testing required by the tumor board. 
 
 

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5.3.2 Study Visits- Cycle 1 Day 8 (± 3 days) 
Subjects will return to the enrolling clinic at Day 8 of cycle 1 for evaluations.  The following 
evaluations will be conducted at those time points: 
1. Physical examination and medical history;  
2. Vital signs, including height, weight, temperature, pulse rate, and sitting blood pressure; 
3. CBC with differential; 
4. Monitoring of AEs;  
5. Review and recording of concomitant medications; 
6. Completion (by study staff) of Case Report Forms; 
7. Any additional labs or testing required by the tumor board. 
 
5.3.3 Study Visits- Cycle 1 Day 15 (± 3 days) 
 
Subjects will return to the enrolling clinic at Day 15 of cycle 1 for evaluations.  The following 
evaluations will be conducted at those time points: 
1. Physical exam and medical history; 
2. Karnofsky Performance status/Lansky Play status-Appendix I; 
3. Vital signs, including temperature, pulse rate, and blood pressure (sitting); 
4. CBC with differential; 
5. Serum electrolytes, BUN, creatinine, Bilirubin, ALT, AST; 
6. Review and recording of concomitant medications; 
7. Monitoring of AEs;  
8. Completion (by study staff) of Case Report Forms; 
9. Any additional labs or testing required by the tumor board. 
 
5.3.4 Study Visits- Cycle 1 Day 22 (± 3 days)-  for 28 day cycles only 
 
Subjects will return to the enrolling clinic at Day 22 of cycle 1 for evaluations.  The following 
evaluations will be conducted at those time points: 
1. Physical examination and medical history;  
2. Vital signs, including height, weight, temperature, pulse rate, and sitting blood pressure; 
3. CBC with differential; 
4. Monitoring of AEs;  
5. Review and recording of concomitant medications; 
6. Completion (by study staff) of Case Report Forms; 
7. Any additional labs or testing required by the tumor board. 
 
 
 

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5.3.5 Subsequent Cycles (Maintenance Protocol Treatment Cycles)  (up to 14 day window 
from end of previous cycle to start Day 1 of the next Cycle treatment per treating 
institutions standard of care) 
 
Drug administration will be according to guidelines in previous cycles with dose modifications if 
needed per Section 5.1.1. The following evaluations will be performed on day 1 of each cycle as 
indicated.  Evaluations may be performed within 5 days prior to dosing unless otherwise 
indicated.  Subsequent cycles (cycles 2 and beyond) may be given at the subject’s home 
institution. If subjects are to receive subsequent cycles at a home institution, this will occur only 
at COG (Children’s Oncology Group) member hospitals or those specifically approved by theSite 
Principal Investigator. 
 
1. Physical examination and medical history; 
2. Karnofsky Performance status/Lansky Play status-Appendix I; 
3. Vital signs, including height, weight, BSA, temperature, pulse rate, and sitting blood 
pressure (same day); 
4. CBC with differential; 
5. Serum electrolytes, BUN, creatinine, Bilirubin, ALT, AST; 
6. LDH and/or Specific Tumor Markers for defined disease (if available); 
7. Review and recording of concomitant medications; 
8. Monitoring of AEs (must be done on Day 1); 
9. Completion (by study staff) of Case Report Forms; 
10. Any additional labs or testing required by the tumor board. 
5.3.6 Reevaluation during Subsequent (Maintenance) Cycles 
Subjects will be assessed for disease at the end of cycle 2 and every other cycle or every 8 
weeks*, whichever occurs first, with the following (timing should be during the last week of 
the cycle):  
1. CT or MRI of measurable disease sites (same scans as done at study entry); 
2. MIBG/PET scan (if indicated for tumor type). Other imaging appropriate for tumor 
type may also be considered; 
3. Any subject with suspected bone marrow disease and with positive bone marrow 
disease at study entry: Bone marrow aspirate and biopsy.  
*After Cycle 6, reevaluations procedures in section 5.3.6 may be done per institutional standard. 
5.3.7 Off Therapy/30 Day Follow-Up Visit 
 
Subjects will be followed up at either the study clinic or by telephone within 30 (+7) days after 
the last dose of treatment. Last dose of treatment is defined as the last day that the subject 
received a tumor board recommended treatment.  The following evaluations will be conducted: 
1. Review and recording of concomitant medications; 
2. Monitoring of AEs and review of concurrent illnesses; 
3. Completion (by study staff) of Case Report Forms.  
Any subject with suspected study drug related toxicities at the follow-up visit must be 
followed until all current drug related adverse events have resolved to baseline or ≤ Grade 2 
or stabilization of the event.  This may require additional clinical assessments and laboratory 

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tests.  The follow-up results will be recorded on the appropriate page of the CRF, as well as 
in the subject's source documentation. 
6 
Protocol Drugs 
Specific treatment details will consist of a regimen chosen from a guided list of agents implicated 
in critical molecular signaling pathways and/or from signature-based predictions of drug efficacy 
summarized from the guided therapy report. All agents are listed in the current pharmacopoeia for 
human use, but will differ amongst individual subjects. The treatment regimens will be discussed 
with families and will include review of known side effects per Pharmacopeia Library (Appendix 
III) (information obtained from package insert and from MicroMedex, LexiComp, Facts and 
Comparisons, and Natural Medicines Database), serious adverse effects of possible new drug 
combinations, and any additional clinical monitoring that may be recommended by the tumor 
board. The family will be given the option to proceed with therapy and if the family decides to 
proceed with the tumor board’s treatment decision they will be asked to sign a treatment specific 
memo.  
 
Drugs will be prescribed by the enrolling institution per treating hospital protocol and 
administered per FDA guidelines and tumor board recommendations.  
 
6.1 
Treatment modifications 
Dosing delays and modifications will be at the discretion of the treating Principal Investigator and 
their institutional pharmacist and based upon the selected therapy, subject response and practiced 
dosing regimens. Decisions will be made on the basis of clinical expertise of the physicians and 
pharmacists and with the subject’s welfare being the principal concern. Informational websites 
such as drug bank (Micromedex, Lexicomp, Facts and Comparisons, Natural Medicines 
Database) will be utilized to identify potential adverse events associated with individual 
treatments. The study pharmacist will be available to consult on decisions made with respect to 
changes and modification made due to potential drug related adverse events. 
 
6.2 
Concomitant Medications and Treatments  
All intercurrent medical conditions will be treated at the discretion of the Investigator according 
to acceptable community standards of medical care. All concomitant medications and treatments 
will be documented on the appropriate case report form.  
 
The following medications are not permitted during the trial:  
• 
Any cytotoxic chemotherapy  
• 
Any other investigational treatment  
• 
Any other systemic anti-neoplastic therapy including, but not limited to, immunotherapy, 
hormonal therapy, targeted therapies, anti-angiogenic therapies, or monoclonal antibody 
therapy  
 
The following medications/treatments may be administered as follows:  
• 
Any radiotherapy administered with palliative intent/pain control or recommended by 
tumor board as part of therapeutic regimen for best patient care. 
• 
Prophylactic filgrastim, pegfilgrastim or oprelvekin; these hematopoietic growth factors 
may be administered according to ASCO, ASH, or institutional guidelines to treat an 
established cytopenia 
o If subject experiences a prolonged neutropenia greater than 72 hours during  
Cycle 1; consider using filgrastim or pegfilgrastim during all subsequent cycles.  

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• 
Erythropoietin, blood products, anti-emetics, steroids, and transfusions may be 
administered at the discretion of the Investigator based on established criteria. 
7 
Efficacy Assessments  
7.1 
Tumor Assessments/Scans  
Tumor assessments/imaging studies must be obtained at baseline, at the end of cycle 2 and again 
after every other cycle (or every 8 weeks, whichever occurs first). After Cycle 6, may be done per 
institutional standard. 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.  
 
All radiological images must be available for source verification. Images may be submitted for 
extramural review for final assessment of antitumor activity.  
Subjects who come off study should have a final end of study disease-specific assessment done 
when possible. 
 
7.2 
Scan Submission:  
All required study scans (CT’s, MRI’s, MIBG’s and PET’s) will be de-identified and sent to the 
NMTRC. All study required de-identified scans will be uploaded to HIPAA compliant database 
(if available) or sent on disc to: 
Alyssa VanderWerff 
NMTRC 
Clinical Program Coordinator 
100 Michigan Avenue NE  MC 272         
Grand Rapids, MI 49503 
Tel:  (616) 267-0327  
E-Mail:  Alyssa.VanderWerff@ helendevoschildrens.org  
7.3 
Response Criteria 
Overall response rate (ORR) in subjects with radiologically assessable disease will be determined 
by CT or MRI by cross-sectional imaging, MIBG/PET scans, and/or bone marrow assessment.  
Response Assessment: Each subject will be classified according to their “best response” for the 
purposes of analysis of treatment effect. Best response is determined from the sequence of the 
objective statuses described below. 
Response Criteria for Subjects with Solid Tumors: This study will use the (RECIST) 
Response Evaluation Criteria in Solid Tumor (version 1.1) from the NCI[44]. Key points are that 
a maximum of 5 target lesions are identified and that changes in the largest diameter (uni-
dimensional measurement) of the tumor lesions are used in the RECIST v1.1 criteria. 
• Measurable disease: The presence of at least one lesion that can be accurately measured in at 
least one dimension with the longest diameter at least 10 mm (CT scan slice thickness no 
greater than 5 mm). The investigator will identify up to 5 measurable lesions to be followed 
for response. Previously irradiated lesions must demonstrate clear evidence of progression to 
be considered measurable. 
• Serial measurements of lesions are to be done with CT or MRI, using the same method of 
assessment is to be used to characterize each identified and reported lesion at baseline and 
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• Quantification of Disease Burden The sum of the longest diameter (LD) for all target lesions 
will be calculated and reported as the disease measurement.   
 
• Complete Response (CR): Disappearance of all target and non-target lesions. 
• Very Good Partial Response (VGPR): Greater than 90% decrease of the disease 
measurement for CT/MRI lesions, taking as reference the disease measurement done to 
confirm measurable disease at study entry. Non-target CT/MRI lesions stable to smaller in 
size. 
• Partial Response (PR): At least a 30% decrease in the disease measurement, taking as 
reference the disease measurement done to confirm measurable disease at study enrollment. 
No new lesions or progression of any non-target measurable lesion.  
• Stable Disease (SD): Neither sufficient decrease to qualify for PR or sufficient increase to 
qualify for PD from study entry. 
• Progressive Disease (PD):  At least a 20% increase in the sum of the disease measurements 
for measurable lesions, taking as reference the smallest disease measurement recorded since 
the start of treatment (nadir), and minimum 5 mm increase over the nadir or the appearance of 
one or more new lesions. 
 
Response Criteria for Subjects with Bone Marrow Disease:  
• Those subjects with morphologic evidence of disease by routine H and E staining (NSE 
staining only is not evaluable) will be evaluable to assess bone marrow response. 
• Complete response: No tumor cells detectable by routine morphology on two consecutive 
bilateral bone marrow aspirates and biopsies done at least three weeks apart after study entry. 
• Progressive disease: Tumor seen on morphology on two consecutive bone marrows done at 
least three weeks apart in subjects who had NO tumor in bone marrow at study entry. (Note: 
Subject may be declared as progressive disease in bone marrow after only one diagnostic bone 
marrow at the discretion of the treating physician after discussion with the study chair.) 
• Stable disease: Persistence of an amount of tumor in the bone marrow by morphology that 
does not meet criteria for either complete response or progressive disease. 
 
Response Criteria for Subjects with MIBG or PET Positive Lesions 
• Subjects who have a positive MIBG or PET scan at the start of therapy will be evaluable for 
MIBG or PET response. All MIBG’s and PET scans will be performed at the research 
institution and then centrally reviewed. 
• Complete response = complete resolution of all positive lesions 
• Partial response = resolution of at least one positive lesion, with persistence of other MIBG 
positive lesions. 
• Stable disease = no change in scan in number of positive lesions (includes subjects who have 
same number of positive lesions but decreased intensity) 
• Progressive disease = Development of new positive lesions 
 
The intensity of MIBG uptake is not to be considered in the above institutional evaluation. 
Duration of response: 
Duration of response is defined as the period of time from when measurement criteria are met for 
complete response (CR) or partial response (PR), whichever is first recorded, until the first date 
that recurrent or progressive disease (PD) is objectively documented (taking as reference for PD 
the smallest measurements recorded since the treatment started). 
The assessment of response will include the initial measurable targets and will be performed after 
the second cycle, then after every other cycle (or 8 weeks, whichever occurs first). Serial results 
of bone marrow aspirates, biopsies and urinary catecholamines will be reviewed for responding 
subjects to confirm response or lack of progression.   

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Clinical Response 
A subject will be defined as having a clinical response if they have stable disease or better and a 
decrease in their tumor markers by ≥ 50%. Clinical response will also be defined as a subject that 
has a complete clearing of a previously positive bone marrow while on study.  
Progression Free Survival 
Time to progression, defined as the period from the first day of administration of study drug until 
the criteria for progression are met taking as reference the screening measurements, will be 
assessed.   
 
8 
Sample Size Justification  
 
Feasibility 
Since this is primarily a feasibility trial, the definition of feasibility for this study will include: 
 
“Enrollment onto study, genomic profile, analysis and report generation completed, tumor 
board held with treatment decision, treatment review completed, start of treatment, and 
completion of 1 cycle of therapy.” 
 
Our preliminary results for 5 subjects indicates that we have a sample collection success rate of 
5/5 (100%) subjects, a genetic report profile success rate of 5/5 (100%) within the 7-10 day time 
window as well as a treatment agreement success rate of 5/5 (100%) within the 5 day time 
window.  The average time (+/-SD) for completion of the genetic profile was 6.6 days (+/-1.7 
days) with a median of 7 days.  The average time (+/-SD) for time to Treatment was 3.2 days (+/-
0.8 days) with a median of 3 days.  Data preliminary to date for each of these three feasibility 
markers are very consistent with our anticipated performance standards.  
  
Our initial feasibility trial continues to show that it is feasible and safe to use RNA expression 
analysis and a DNA mutation panel for tumor boards creating treatment decisions for patients 
without curative options. This study will ask the feasibility of utilizing DNA exomes and RNA 
sequencing in a tumor for molecular guided therapy. 
 
 
Assumptions:  The feasibility outcome is a binary measure for each of the three clinical strata 
with a lower success null value of 50% which would require reconsideration of the full process 
and an upper success value of 75% for the alternative which would be deemed worthy of further 
consideration for an efficacy trial at the next phase. A binomial distribution was used for the 
testing process with a combination of Type I error levels (10%) and Power (75%).  The basic 
design overall is a MiniMax approach which minimizes the overall sample size. The MiniMax 
design with an interim look will require an overall sample size of n = 16.  Each of the three 
clinical strata will use a two-stage decision rule. 
 
The Two-Stage Stopping Rule for each of the three strata is as follows: 
 
Stage 1: Stop and accept the null hypothesis if the observed feasibility rate is less than or equal to 
5/9.  Otherwise, continue to stage 2. 
 
The probability of stopping for futility is 0.746 when Ho is true and 0.166 when Ha is true. 
 

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Stage 2: Stop and accept the null hypothesis if the observed feasibility rate is less than or equal to 
10/16.  Otherwise, stop and reject the null hypothesis. 
 
As of Amendment 3.0, 100 subjects have been enrolled and all feasibility measures for all strata 
have been met.  To gain additional feasibility with the new Drug Prediction Report and additional 
safety and efficacy data, additional subjects will be enrolled to meet a revised goal of 200 total 
evaluable subjects. 
 
The expanded access for 100 patients will enroll following implementation of Amendment 
3.0.  Their tumor samples will be analyzed using an updated Drug Prediction Report (Appendix 
III).  Overall Response Rate (ORR) and Progression Free Survival (PFS) for this group will be 
compared to those of the first 100 patients who received treatment based upon the original Drug 
Prediciton Report and Pharmacopeia Library. 
 
9 
Laboratory Evaluations 
9.1 
Specimens to be Collected, Schedule and Amount 
Required samples will be collected at the start of study. Recommended/Secondary 
(volunteer/optional) samples will also be collected at the start of study. Additionally, optional 
bone marrow samples will be collected every 6-8 weeks per Study Procedure Table. 
 
9.2 
Tumor collection and correlative biology studies. 
 
Fresh tumor will be flash frozen and placed in kit for Ashion along with 4-6ml blood sample in an 
EDTA tube. Viable, fresh tumor from tumor biopsy should be placed in cell growth media using 
sterile technique for, cell line and xenograft generation, one vial of tumor in RNA later, and two 
vials of fresh frozen tumor to be shipped to the Pediatric Oncology Translational Research 
Laboratory for RNA analysis. Samples should be labeled with subject’s study number, date of 
extraction and sample contents. If excess tissue is available, then snap frozen tumor tissue 
approximately 5mm in size should be wrapped in foil, snap frozen in liquid nitrogen and stored at 
-80ºC. Tissue samples will be coded. Fixed tissue remaining from diagnostic evaluation may be 
used.  Bone marrow samples will also be sent to the Pediatric Oncology Translational 
Research Laboratory for tumor cell isolation and culture. 
 
At the Pediatric Oncology Translational Research Laboratory tumor cells will be grown to 70% 
confluency in cell growth media. Cell lines will be maintained in culture for biology studies. 
These will include determining the growth curves and responsiveness of cells derived from these 
tumors to a variety of agents identified on the report in vitro (both the chosen regimen as well as 
alternate options). Cells will be injected into the inguinal fat pad of NOD SCID mice for 
generation of subject xenografts. These mice will be used for correlative drug testing experiments 
based on predictive models. Evaluation of mechanism of action of new drug combinations will be 
evaluated in mice models and in cell culture through immunohistochemical staining, 
phosphoproteomics, PCR, and western blotting. These models will allow us the opportunity to 
evaluate alternate drug combinations that might have been superior to the chosen regimen.  
 
 

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9.3 
Detailed Procedure For Sending Subject Samples: 
 
At screening, subjects will have biopsy samples sent. The main sample for study report will be 
referred to as the “Primary Sample.”  
 
The “Primary Sample” will be a current solid tumor biopsy or core bone marrow biopsy (with 
>50% viable tumor) along with a 4-6 mL blood sample collected in an EDTA tube. 
 
If a solid tumor sample cannot be obtained and the subject’s bone marrow is <50% tumor then 
they will be ineligible for study. 
 
In addition to the “Primary Sample”, if subjects have signed the additional consent for optional 
sample collection, they will also have these secondary samples sent as follows.  
 
9.3.1 Sample Procurement and Shipping at Screening:   
 
De-identified subject tumor samples will be sent on all subjects as following: 
 
Label all tubes with subject’s unique identifier, date/time of sample collection, and 
contents (i.e. solid tumor, bone marrow, blood). 
 
9.3.1.1 Send the following Required Primary Samples for All Tumor Types (along with 
appropriate form) 
 
1. Required- Sample 1 (tumor) 
 
Solid Tumor or Bone Marrow Core Biopsy (if solid tumor is not available)- 
You will be provided a kit for tumor collection.  This kit will include 
instructions, collection tubes and shipping instructions.  
 
For sample 1 follow collection instructions in Appendix II (flash freeze tumor 
sample within 20 minutes of harvest, or sooner when possible) and ship 
overnight on at least 1kg of dry ice to: 
 
 
*Note: Do NOT place sample in aluminum/tin foil at any time. 
 
Ashion Analytics, LLC  
445 N 5th Street, Suite 468 
Phoenix, AZ 85004 
Phone: 602-343-8796  
Lab Fax: 602-343-8545 
email: customerservice@ashiondx.com 
 
For Biopsies- refer to Instructions for Core/Needle Biopsy Specimens for sample 
size instructions.  
For Surgical resections- size of sample should be about the size of a pencil 
eraser. Minimum amount of tumor sample required is 50-200 mg of tissue.  
 
 

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2. Required- Sample 2 (blood): 
Send 4-6 mL of blood in EDTA tube (ambient – prefer to have shipped on frozen 
gel pack in summer months May to October) to: 
Ashion Analytics, LLC 
445 N 5th Street, Suite 468 
Phoenix, AZ 85004 
Phone: 602-343-8796  
Lab Fax: 602-343-8545 
email: customerservice@ashiondx.com 
 
 
9.3.1.2 Send the following Recommended secondary tumor samples along with appropriate 
forms listed in order of priority (please work your way down the list of tumor samples 
until you either run out of available sample or have completed all samples. Once this 
occurs move on to Bone Marrow samples: 
 
 
You will be provided a kit for tumor collection (fresh snap frozen and in culture 
media).  Follow collection instructions and ship as directed overnight.  
 
3. Sample 3: 
 
With sterile technique and within 20 minutes add tumor sample or needle core biopsy 
to T25 flask containing cell growth media (provided), seal with parafilm, and 
overnight at ambient temperature to: 
Ping Zhao  
Pediatric Oncology Translational Research Laboratory  
Coopers Landing 
1345 Monroe Ave, Suite 121 
Grand Rapids, MI 49505  
Ph: 616-486-8645 
Ping.zhao@helendevoschildrens.org 
 
4. Sample 4: 
 
Add tumor or needle core biopsy to cryo-vial, snap freeze and ship on at least 1kg of 
dry ice to: 
Ping Zhao  
Pediatric Oncology Translational Research Laboratory  
Coopers Landing 
1345 Monroe Ave, Suite 121 
Grand Rapids, MI 49505 
Ph: 616-486-8645 
Ping.zhao@helendevoschildrens.org 
 
 
 

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5. Sample 5: 
Add tumor or needle core biopsy to cryo-vial, snap freeze and ship on at least 1kg of 
dry ice to: 
Ping Zhao  
Pediatric Oncology Translational Research Laboratory  
Coopers Landing 
1345 Monroe Ave, Suite 121 
Grand Rapids, MI 49505 
Ph: 616-486-8645 
Ping.zhao@helendevoschildrens.org 
 
 
6. Sample 6: 
Add tumor or needle core biopsy to RNA Later and ship overnight at ambient 
temperature to: 
Ping Zhao  
Pediatric Oncology Translational Research Laboratory  
Coopers Landing 
1345 Monroe Ave, Suite 121 
Grand Rapids, MI 49505  
Ph: 616-486-8645 
Ping.zhao@helendevoschildrens.org 
 
 
 
9.3.1.3 For all Tumor Types: Send the following Recommended secondary blood sample 
(along with appropriate forms): 
 
Blood-  Send 4-6 mL of blood in  tubes (tubes and instructions will be provided). 
 
1. Sample 7: 
Send PAX DNA Gene tubes (ambient) to: 
 
Ping Zhao 
Pediatric Oncology Translational Research Laboratory  
Coopers Landing 
1345 Monroe Ave, Suite 121 
Grand Rapids, MI 49505  
Ph: 616-486-8645 
Ping.zhao@helendevoschildrens.org 
 
 
 
 

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9.3.1.4 For Neuroblastoma Subjects or Any subject with suspected bone marrow disease 
Only- Send the following Recommended secondary bone marrow samples listed in 
order of priority (along with appropriate forms): 
 
1. Sample 8: 
 
Bone Marrow Aspirate- Send 4 mL of bone marrow aspirate (preferably bilateral) 
in green top (sodium heparin) tube(s) priority overnight at room temperature to: 
 (Please alert site 2-3 days prior to procedure.  Contact site to confirm shipment as 
well.) 
 
Ping Zhao  
Pediatric Oncology Translational Research Laboratory  
Coopers Landing 
1345 Monroe Ave, Suite 121 
Grand Rapids, MI 49505  
Ph: 616-486-8645 
Ping.zhao@helendevoschildrens.org 
 
 
 
Notes:  If all samples are collected, you will be collecting 8 samples and mailing 4 
packages.  The samples above are listed in decreasing priority. 
 
* Sample 1 to Ashion (frozen on dry ice) 
** Sample 2 to Ashion (ambient with frozen gel pack) 
***Sample 3, 6, 7, & 8 to Pediatric Oncology Translational Research Laboratory 
(ambient). 
****Samples 4 & 5 to Pediatric Oncology Translational Research Laboratory (frozen). 
 
******* Keep collection flask (sample 3) at 4° C. until ready to use. 
 
Please contact Ping Zhao if you have any trouble with the preparation or packaging of the 
samples.   Ping.zhao@helendevoschildrens.org 
 
 
 

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9.3.2 For Neuroblastoma Subjects or Any subject with suspected bone marrow disease 
Only- Sample Procurement and Shipping at the end of Cycle 2 and every two cycles 
after that:   
 
Send the following Recommended samples (along with appropriate forms) to the  
Pediatric Oncology Translational Research Laboratory   
 
1. Bone Marrow Aspirate- Send 4 mL of bone marrow aspirate (preferably bilateral) 
in green top (sodium heparin) tube(s) priority overnight at room temperature to: 
 
Ping Zhao  
Pediatric Oncology Translational Research Laboratory 
Coopers Landing 
1345 Monroe Ave, Suite 121 
Grand Rapids, MI 49505  
Ph: 616-486-8645 
Ping.zhao@helendevoschildrens.org 
 
9.4 
Storage 
 
Blood and tumor samples collected for any studies performed in this protocol, and any 
other components from the processed cells, may be stored indefinitely to research 
scientific questions related to cancer and/or study drugs. The subject retains the right to 
have the sample material destroyed at any time by contacting the principal investigator. 
 
 
 
 
 
 
 
 
 
 

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9.5 
Plan for Communication of Samples and Data 
 
 

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9.6 
Plan for Communication of Collaborating Sites 
Communication between centers will be critical in this trial.  Prior to consent of the subject, the 
NMTRC research coordinator will be contacted (via e-mail). If a spot is available at the time, the 
potential subject will undergo consent and completion of all required screening procedures and 
certification of all inclusion and exclusion criteria by the Investigator.  If the subject fits all 
enrollment criteria, the site will again contact the coordinator at the NMTRC who will notify 
TGen, Ashion, Spectrum Health, and the Pediatric Oncology Translational Research Laboratory 
in preparation for collection and processing of tissue sample. The research coordinator at 
NMTRC will organize the convening of members of the tumor board for discussion of the current 
case once the full report is available. In addition, a study enrollment form will be faxed to the 
coordinator at NMTRC, a unique subject identifier will be assigned and the enrollment form will 
be sent back to the participating site. The NMTRC will contact all sites via e-mail if the study 
enrollment is on hold or closed at any time. 
 
Subject samples will be collected at each institution and follow the flow chart above.  Once the 
reports are generated they will be sent to NMTRC/Dr. Sholler. The Principal Investigator 
enrolling the patient will prepare a tumor board presentation. The presentation and reports will be 
sent to all tumor board members by the NMTRC coordinator.  There will be a meeting of the 
tumor board within 4 days of receiving the report to decide on the treatment plan 
recommendation. The recommendation will be reviewed in depth for safety by the Pharmacist. 
The treatment plan and memo will be discussed with the subject and their parents and upon their 
signed agreement the treatment will begin within 1 week of the discussion with parents.   
  
 
Each site will also participate in a 1 hour monthly video or teleconference meeting to review 
study progress and subjects currently enrolled. There will also be a yearly face-face study 
committee meeting hosted by a member institution. 
 
10 ADVERSE EVENT REPORTING 
10.1 
 Definitions 
10.1.1 Adverse Event 
An adverse event is any untoward medical occurrence in a subject or clinical investigation subject 
administered a pharmaceutical product and which does not necessarily have to have a causal 
relationship with this treatment.  An adverse event can therefore be any unfavorable and 
unintended sign (including an abnormal laboratory finding, for example), symptom, or disease 
temporally associated with the use of a medicinal product, whether or not considered related to 
the medicinal product. 
An untoward medical event which occurs outside the period of follow-up as defined in the 
protocol will not be considered an adverse event unless related to study drug.  Worsening of a 
medical condition for which the efficacy of the study drug is being evaluated will not be 
considered an adverse event.  
 
10.1.2 Unexpected Adverse Event 
An unexpected adverse event is one for which the nature or severity of the event is not consistent 
with the applicable product information as outlined in package insert filed with the FDA. 
 

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10.1.3 Serious Adverse Event 
A serious adverse event is any untoward medical occurrence that: 
• 
Results in death 
• 
Is life-threatening (an event in which the subject was at risk of death at the time of the 
event; it does not refer to an event which hypothetically might have caused death if it were 
more severe) 
• 
Requires in-patient hospitalization or prolongation of existing hospitalization 
• 
Results in persistent or significant disability/incapacity 
 
• 
Results in a congenital anomaly or birth defect 
• 
Other important medical events that may not be immediately life-threatening or result in 
death or hospitalization but may jeopardize the subject or may require intervention to 
prevent one of the other outcomes listed above.  Examples of such events are intensive 
treatment in an emergency room for allergic bronchospasm; blood dyscrasias or 
convulsions that do not result in hospitalization; or development of drug dependency or 
drug abuse. 
 
The term “severe” is often used to describe the intensity (severity) of an event; the event itself 
may be of relatively minor medical significance (such as a severe headache).  This is not the same 
as “serious”, which is based on subject/event outcome or action criteria usually associated with 
events that pose a threat to a subject’s life or functioning.    
10.1.4 Documenting Adverse Events  
The Investigator should elicit information regarding the occurrence of adverse events through 
open-ended questioning of the subject, physical examination and review of laboratory results.   
 
All adverse events, whether serious or not, will be described in the source documents and Grade 3 
or higher (per CTCAE 4.0) related and unexpected adverse events that occur while on study 
should be captured on the adverse event case report form.  All Baseline AE’s will be captured on 
a separate baseline Adverse event case report form. All Grade 3 or higher related and unexpected 
new events, as well as those that worsen in intensity or frequency relative to baseline, which 
occur after administration of study drug through the period of protocol-specified follow-up, must 
be captured. 
 
Information to be reported in the description of each adverse event includes: 
• 
A medical diagnosis of the event (if a medical diagnosis cannot be determined, a 
description of each sign or symptom characterizing the event should be recorded)  
• 
The date of onset of the event and relatedness to treatment regimen. 
• 
The date of resolution of the event and whether the event is serious or not 
• 
Action taken; drug treatment required; non-drug treatment required; hospitalization or 
prolongation of hospitalization required; diagnostic procedure performed; subject 
discontinued from the study 
• 
Outcome: complete recovery or return to baseline; unknown/lost to follow-up; adverse 
event persisting; subject died (notify the NMTRC immediately)   
 
Adverse events will be collected for 30 days following the last treatment or until a new treatment 
is started. Suspected study drug-related toxicity at the 30 day follow-up visit must continue to be 
followed until resolution to baseline or ≤ Grade 2 or stabilization of the event.  
 

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10.1.5 Expedited Reporting of Serious Adverse Events 
All fatal or life–threatening adverse events must be reported to the NMTRC immediately by 
telephone, fax, or e-mail within 24 hours of knowledge of the event. If full information is not 
known, additional follow-up by the Investigator will be required. 
 
All other serious adverse events that are related and unexpected (not listed in the relevant 
appendices) which occur any time after the subject has been consented up to 30 days after the last 
dose of treatment, and are possibly, probably, or definitely related to the research must be 
reported to the study chair and appropriate regulatory authorities (local IRB and FDA if required) 
within 7 days of notification of the event. 
 
 
The Investigator must report all serious adverse events reported to regulatory authorities in an 
expedited manner to the local IRB or IEC.  All serious adverse events must be followed until 
resolution or stabilization.   Unanticipated problems involving risk to subjects or others, serious 
adverse events related to participation in the study, and all volunteer deaths related to 
participation in the study should be promptly reported to the NMTRC. 
 
NMTRC Reporting Contact 
Please report all expedited reports to: 
 
Alyssa VanderWerff and Genevieve Bergendahl, RN 
NMTRC 
Tel:  (616) 267-0327  
E-Mail:  Alyssa.VanderWerff@helendevoschildrens.org 
E-Mail:  Genevieve.Bergendahl@helendevoschildrens.org 
 
10.1.6 Grading and Relatedness of Adverse Events 
10.1.6.1 Grading of Severity of an Adverse Event 
Each adverse event (Grade 2 or higher) will be graded for severity per the National Cancer 
Institute Common Terminology Criteria for Adverse Events (CTCAE V 4.0), and these criteria 
must be used in grading the severity of adverse events.  The criteria can be found at: 
http://ctep.cancer.gov/reporting/ctc.html. 
 
Grading of Severity of an Adverse Event Not Listed in Published Criteria: 
For those adverse events which are not listed as part of the NCI CTCAE V 4.0, the same grading 
system should be used, where: 
• 
Mild corresponds to an event not resulting in disability or incapacity and which resolves 
without intervention 
• 
Moderate corresponds to an event not resulting in disability or incapacity but which 
requires intervention 
• 
Severe corresponds to an event resulting in temporary disability or incapacity and which 
requires intervention 
• 
Life-threatening corresponds to an event in which the subject was at risk of death at the 
time of the event 
• 
Fatal corresponds to an event that results in the death of the subject 
 

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10.1.6.2 Relatedness to Study Drug 
The Investigator must attempt to determine if an adverse event is in some way related to the use 
of the study drug and define an attribution category. This relationship should be described as 
follows: 
 
RELATIONSHIP 
ATTRIBUTION 
DESCRIPTION 
Unrelated to 
investigational 
agent/intervention 
 
Unrelated 
The AE is clearly NOT related to the 
intervention. 
The event is clearly due to causes distinct from the use of 
the study drug, such as a documented pre-existing 
condition, the effect of a concomitant medication, or a new 
condition which, based on the pathophysiology of the 
condition, and the pharmacology of the study drug, would 
be unrelated to the use of the study drug. 
Unlikely 
The AE is doubtfully related to the intervention. 
Adverse event does not have temporal relationship to 
intervention, could readily have been produced by the 
subject’s clinical state, could have been due to 
environmental or other interventions, does not follow 
known pattern of response to intervention, does not 
reappear or worsen with reintroduction of intervention. 
Related to 
investigational 
agent/intervention 
 
Possible 
The AE may be related to the intervention. 
The event follows a reasonable temporal sequence from 
administration of the study drug and the event follows a 
known response pattern to the study drug BUT the event 
could have been produced by an intercurrent medical 
condition which, based on the pathophysiology of the 
condition, and the pharmacology of the study drug, would 
be unlikely related to the use of the study drug OR the 
event could be the effect of a concomitant medication. 
Probable 
The AE is likely related to the intervention. 
The event follows a reasonable temporal sequence from 
administration of the study drug, the event follows a 
known response pattern to the study drug AND the event 
cannot have been reasonably explained by an intercurrent 
medical condition OR the event cannot be the effect of a 
concomitant medication. 
Definite 
The AE is clearly related to the intervention. 
The event follows a reasonable temporal sequence from 
administration of the study drug, the event follows a 
known response pattern to the study drug and based on the 
known pharmacology of the study drug, the event is 
clearly related to the effect of the study drug.  The adverse 
event improves upon discontinuation of the study drug and 
reappears upon repeat exposure. 
 
 
 
 

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11 SUBJECT WITHDRAWAL AND TRIAL DISCONTINUATION 
11.1 
Criteria for Subject Off-Therapy 
Subjects will be removed from the study therapy for the following reasons: 
• 
Subject completes protocol defined therapy (a minimum of one cycle)  
• 
Progressive neoplastic disease 
• 
Subject or guardian withdraws consent to continue in the trial 
• 
Subject develops an intercurrent illness that precludes further participation, or requires a 
prohibited concomitant treatment 
• 
The Investigator withdraws the subject in the subject’s best interests 
• 
Subject is lost to follow-up (defined as the inability to contact the subject on 3 separate 
occasions over a period of 2 weeks) 
• 
Administrative reasons (e.g., the subject is transferred to hospice care) 
• 
An adverse event, which in the opinion of the Investigator, precludes further trial 
participation or fulfills the protocol requirements for withdrawal  
• 
Death 
 
11.2 
Criteria for Subject Off-Study 
Subjects may be withdrawn from the study completely which includes withdrawal from survival 
follow-up for the following reasons: 
• 
Completion of all study requirements 
• 
Subject or guardian withdraws consent to continue in the trial (if this occurs, no further 
study visits or data may be collected) 
• 
Subject is lost to follow-up (defined as the inability to contact the subject on 3 separate 
occasions over a period of 2 weeks) 
• 
Death 
 
11.3 
Trial Discontinuation  
The Neuroblastoma and Medulloblastoma Translational Research Consortium (NMTRC) may 
discontinue the trial as a whole or at an individual investigational site at any time. Reasons for 
early trial discontinuation may include, but are not limited to, unacceptable toxicity of 
treatment regimens, a request to discontinue the trial from a regulatory authority, protocol 
violations at an investigational site, violations of good clinical practice at an investigational 
site, or poor enrollment. The NMTRC will promptly inform all Investigators in the event of 
premature study discontinuation and provide all Investigators with instructions regarding the 
disposition of subjects still on study. Should the study be terminated prematurely, all case 
report forms and any other study material will be returned to the NMTRC.  
 
12 DATA ANALYSIS   
12.1 
Data Quality Assurance  
Electronic and paper case report forms will be checked for correctness against source document 
data by the independent study monitor. If any entries into the CRF are incorrect, incomplete or 

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illegible, the study monitor will ask the Investigator or the study site staff to make appropriate 
corrections.  
12.2 
Data Safety Monitoring Board (DSMB)  
An independent Data Safety and Monitoring Board (DSMB) will oversee the conduct of the 
study. The members of this Board will receive database summaries, including adverse event 
reports, and will convene either in person or via teleconference according to section 3.5. The 
Board will be responsible for decisions regarding possible termination and/or early reporting of 
the study.  
12.3 
Process and Feasibility Analysis 
Each of the process measures including the total time to treatment initiation and time to 
completion of the first cycle of treatment will be described using standard descriptive methods 
such as means, medians, standard deviations, and 95% confidence intervals.  The total time 
duration to treatment initiation and time to completion of the first cycle of treatment will also be 
examined using Kaplan-Meier plots since some patients who are considered process failures or 
who do not complete the full duration to the completion of the first cycle of treatment may 
contribute censored data.  The formal hypothesis testing of the feasibility or success is based upon 
the 2-stage Mini-Max testing process outlined in Section 8: Sample Size Justification.  Further 
quantification of the feasibility success rate will be based upon the percentage of the n = 16 
patients in each strata who achieve the specified overall time frame limits.  This success rate will 
be supplemented with an exact 95% confidence interval using a Binomial distribution model due 
to the small sample size involved.  
12.4 
Secondary Data Analysis 
Overall response rates (ORR) will be examined using rates for each of the clinical response 
categories supplemented using exact 95% confidence intervals.  Progression free survival (PFS) 
data for each of the three clinical strata will be examined using Kaplan-Meier time to event plots.  
Differences in the PFS for the current treatment protocol with historical PFS values will be 
explored using Cox proportional hazard rate methods when possible. Patients that enroll through 
compassionate access will be included in secondary data analysis. 
 
13 ADMINISTRATIVE PROCEDURES  
13.1 
Subject Informed Consent  
No study related procedures will be performed until a subject or a subject’s legal representative 
has given written informed consent. The NMTRC will provide the site Investigators with a 
sample informed consent document that conforms to all the requirements for informed consent 
according to ICH GCP and US FDA guidelines (21 CFR 50). However, it is up to each site 
Investigator to provide a final informed consent that may include additional elements required by 
the Investigator’s institution or local regulatory authorities. The IRB/EC for each investigational 
site must approve the consent form document prior to study activation; changes to the consent 
form during the course of the study may also require IRB/EC approval. The informed consent 
document must clearly describe the potential risks and benefits of the trial, and each prospective 
participant must be given adequate time to discuss the trial with the Investigator or site staff and 
to decide whether or not to participate. Each subject who agrees to participate in the trial and who 
signs the informed consent will be given a copy of the signed dated and witnessed document. The 
original copy of the signed dated and witnessed informed consent document will be retained by 

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the Investigator in the study files. After the tumor board has made a therapy decision and that 
decision has been reviewed by the pharmacist, a therapy specific treatment memo will be signed. 
 
The Investigator must also obtain authorization from the subject to use and/or disclose protected 
health information in compliance with the Health Insurance Portability and Accountability Act 
(HIPAA). Written HIPAA authorization may be obtained as part of the informed consent process.  
 
13.2 
Ethical Conduct of the Study and IRB/IEC Approval  
The study will be conducted according to the principles of the 2004 version of the Declaration of 
Helsinki, the International Conference on Harmonization Guidance on Good Clinical Practice and 
the requirements of all local regulatory authorities regarding the conduct of clinical trials and the 
protection of human subjects.  
 
The Investigator will submit the protocol, the informed consent and any other material used to 
inform subjects about the trial to the local IRB/IEC for approval prior to enrolling any subject 
into the trial. The IRB/IEC should be duly constituted according to applicable regulatory 
requirements. Approval must be in the form of a letter signed by the Chairperson of the IRB/IEC 
or the Chairperson’s designee, must be on IRB/IEC stationary and must include the protocol by 
name and/or designated number. If an Investigator is a member of the IRB/IEC, the approval 
letter must stipulate that the Investigator did not participate in the final vote, although the 
Investigator may participate in the discussion of the trial. The Investigator will also inform the 
IRB/IEC of any serious adverse events that are reported to regulatory authorities and will provide 
to the IRB/IEC a final summary of the results of the trial at the conclusion of the trial.  
 
Any amendments to the protocol will be done through the NMTRC, and will be submitted to the 
coordinating IRB/IEC for review and written approval before implementation.  
 
13.3 
Monitoring  
An independent study monitor will make regularly scheduled trips to the investigational site to 
review the progress of the trial. The actual frequency of monitoring trips will depend on the 
enrollment rate and performance at each site. At each visit, the monitor will review various 
aspects of the trial including, but not limited to, screening and enrollment logs; compliance with 
the protocol and with the principles of Good Clinical Practice; completion of case report forms; 
source data verification; facilities and staff.  
 
During scheduled monitoring visits, the Investigator and the investigational site staff must be 
available to meet with the study monitor in order to discuss the progress of the trial, make 
necessary corrections to case report form entries, respond to data clarification requests and 
respond to any other trial-related inquiries of the monitor.  
 
In addition to the above, representatives of the NMTRC or government inspectors may review the 
conduct/results of the trial at the investigational site. The Investigator at each site must promptly 
notify the NMTRC of any audit requests by regulatory authorities.  
 
A separate monitoring plan will be provided for additional monitoring guidelines.  
 

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13.4 
Pre-Study Documentation  
Prior to initiating the trial, the Investigators at each site will provide to the NMTRC the following 
documents:  
• A signed NMTRC009 Investigator Agreement Form 
• A current curriculum vitae for the Principal Investigator and each sub-investigator listed on the 
Investigator Agreement Form 
• A copy of the Investigator’s medical license from the state in which the study is being 
conducted 
• A letter from the IRB or EC stipulating approval of the protocol, the informed consent 
document and any other material provided to potential trial participants with information about 
the trial (e.g., advertisements)  
• A copy of the IRB- or EC-approved informed consent document  
• Current IRB membership list for IRB’s without a multiple project assurance number or an IRB 
organization number under the Federal Wide Assurance program (www.ohrp.osophs.dhhs.gov).  
• A signed Investigator Signature Sheet for each amendment put through local IRB- Found on 
page 9 of this protocol (original) 
• A completed conflict of interest and financial disclosure form (copy of original) from each 
person listed in the Investigator Agreement Form.  
• Current laboratory certification for the reference laboratory  
• A list of current laboratory normal values for the reference laboratory  
13.5 
Confidentiality  
It is the responsibility of the investigator to insure that the confidentiality of all subjects 
participating in the trial and all of their medical information is maintained. Case report forms and 
other documents submitted must never contain the name of a trial participant. Each subject in the 
trial will be identified by a unique identifier that will be used on all CRF’s and any other material 
submitted to the NMTRC. Case Report Forms for this study will be both paper and electronic. 
Electronic data will be stored in a HIPAA compliant data center. All case report forms and any 
identifying information must be kept in a secure location with access limited to the study staff 
directly participating in the trial.  
 
Personal medical information may be reviewed by representatives of the NMTRC, of the IRB or 
of regulatory authorities in the course of monitoring the progress of the trial. Every reasonable 
effort will be made to maintain such information as confidential.  
 
The results of the study may be presented in reports, published in scientific journals or presented 
at medical meetings; however, subject names will never be used in any reports about the study.  
 
13.6 
Source Documents  
The Investigator will maintain records separate from the case report forms in the form of clinical 
charts, medical records, original laboratory, radiology and pathology reports, pharmacy records, 
etc. The Investigator will document in the clinic chart or medical record the name and number of 
the trial and the date on which the subject signed informed consent prior to the subject’s 
participation in the trial. Source documents must completely reflect the nature and extent of the 
subject’s medical care, and must be available for source document verification against entries in 

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the case report forms when the monitor visits the investigational site. All information obtained 
from source documents will be kept in strict confidentiality.  
 
13.7 
Record Retention  
The Investigator will retain the records of the study for 15 years.  The NMTRC will notify 
Investigators when retention of study records is no longer required. All study records must be 
maintained in a safe and secure location that allows for timely retrieval, if needed.  
 
Study records that must be retained include copies of case report forms, signed informed 
consents, correspondence with the IRB or IEC, source documents, clinic charts, medical records, 
laboratory results, radiographic reports and screening/enrollment logs.  
 
Should the Investigator relocate or retire, or should there be any changes in the archival 
arrangements for the study records, the NMTRC must be notified. The responsibility for 
maintaining the study records may be transferred to another suitable individual, but the NMTRC 
must be notified of the identity of the individual assuming responsibility for maintaining the study 
records and the location of their storage. 
 
 
 
 
 
 
 
 
 
 

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Appendix I: Performance Status/Scores 
 
 
 
 
 
 
 
 
 
 
 
 
 

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Appendix II: Biology Studies Collection and Shipping forms 
Instructions for Core/Needle Biopsy Specimens 
Interventional Radiologist: 
Standard Pathology Sample 
1. Obtain first core biopsy (if possible; otherwise 2nd core) 
a. At least 18 gauge guiding needle or larger in caliber 
b. Remove excess blood from the sample with sterile saline rinse (provided 
in the kit) without damaging the sample 
 
2. Place core (for standard pathology) in neutral buffered formalin container per 
standard practices 
 
3. Send tissue to pathology 
 
       Primary Sample – sent to Ashion 
4. Obtain second core biopsy from same track according to institutional protocol 
 
5. DO NOT PLACE SAMPLE INTO FORMALIN. Flash Freeze sample within 20 
minutes of extraction and place in Tube 1 provided by the NTMRC. Note time of 
extraction and time of flash freezing. 
 
6. Upon generation of a pathology report, please e-mail the NMTRC with the 
percent tumor in Sample 1.         
 
Pathologist: 
Place Tube 1 with the patient sample and Ashion Shipping Form in the shipping 
kit.  Affix the label to FedEx shipping bag and place the kit in the bag for 
shipment.  Please ship via FedEx (if you do not have a scheduled FedEx pickup, 
call 800-GO-FEDEX - 800-463-3339). 
 
Note- Ashion is unable to generate a patient molecular report without knowing 
the percent viable tumor in the sample (Must be >50% to move forward) - 
Thank you 
For questions please call the NMTRC at (616) 267-0327 or e-mail 
nmtrc@helendevoschildrens.org  

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Instructions for Incision/Excision Surgery Specimen 
Surgeon: 
1. Obtain surgical excision/biopsy (operating room or office) 
a. DO NOT PLACE SAMPLE INTO FORMALIN 
b. Please place sample directly (not wrapped) into the provided sterile 
saline (0.9% NaCl without dextrose), place in a labeled container and note 
time of extraction on container label. 
 
2. Send to Pathology/Histology ASAP; please hand deliver to pathology within 20 
minutes.  NEVER AT ANY TIME PUT SAMPLE IN TIN/ALUMINUM FOIL. 
Pathologist/Pathology Assistant: 
1. Do not ink specimen (prior to completing steps 2-4 below) 
 
2. Section specimen with a sterile blade on a clean surface.  Select tumor tissue 
that appears non-necrotic; avoid normal tissue.  Obtain a specimen for 
histopathological analysis at your institution, avoiding normal or necrotic tissue. 
 
3. Obtain a sample with a maximum dimension of 0.5 cm3 (approximately the size 
of a pencil eraser).  Minimum amount of tumor sample required is 50-200mg of 
tissue.   
 
4. Flash Freeze sample within 20 minutes of extraction and place in Tube 1 
provided by the NTMRC. Note time of time of flash freezing. 
 
5. Place Tube 1 with the patient sample and Ashion shipping form in the shipping 
box with dry ice.  Affix a shipping label to the FedEx shipping bag and place the 
kit in the bag for shipment.  Please ship via FedEx (if you do not have a scheduled 
FedEx pickup, call 800-GO-FEDEX - 800-463-3339)   
 
6. Handle any remaining tissue as per your institutional protocols and in 
accordance with physician order 
 
7. Upon generation of a pathology report, please e-mail the NMTRC with the 
percent tumor in Sample 1.           
 
Note- Ashion is unable to generate a patient molecular report without knowing the 
percent viable tumor in the sample (Must be >50% to move forward) - Thank you 
For questions please call the NMTRC at (616) 267-0327 or e-mail 
nmtrc@helendevoschildrens.org 

Clinical Protocol NMTRC009 
 
Version 3.0 FINAL 
Page 67 of 70 
Confidential 
Issued 10 January 2017  
Appendix III: Pharmacopeia Library 
Drug Table: 
 
 
 
 
Acetazolamide 
Dinutuximab 
Leflunomide 
Raloxifene hydrochloride 
Adalimumab 
Docetaxel 
Lenalidomide 
Ramipril 
Albendazole 
Donepezil  
Lomustine 
Rifampin 
Aldesleukin 
DOXOrubicin 
Lovastatin 
Rituxumab 
Alemtuzumab 
Doxycycline 
Luteolin 
Romidepsin 
Alfuzosin 
Enalapril 
Mechlorethamine 
Rosuvastatin calcium 
Anakinra 
Epirubicin 
Mercaptopurine 
Ruxolitinib 
Anastrozole 
Ergocalciferol 
Mesalamine 
Simvastatin 
Atorvastatin 
Eribulin 
Methotrexate 
Sirolimus  
Atovaquone 
Erlotinib 
Methyl CCNU 
Sorafenib 
Azacitidine 
Ethambutol 
MitoMYCIN 
Streptozocin 
Balsalazide 
Ethosuximide 
Mitotane 
Sulfasalazine 
Bevacizumab 
Etodolac 
Mitoxantrone 
Sulindac 
Bexarotene 
Etoposide  
MK4 
Sunitinib 
Bortezomib  
Everolimus 
Nabumetone 
Tacrolimus 
Brentuximab 
Famotidine 
Naproxen 
Tamoxifen 
Bumetanide 
Felodipine 
Nelarabine 
Temozolomide 
Bupropion 
Fenoprofen 
Nilotinib 
Temsirolimus 
Capecitabine 
Fexofenadine 
Nivolumab 
Teniposide 
Captopril 
Flucytosine 
Octreotide 
Thalidomide 
Carboplatin 
Fludarabine 
Ofatumumab 
Thioguanine 
Carmustine 
Fludrocortisone 
Olaparib 
Thiotepa 
Celecoxib 
Fluorouracil 
Omeprazole 
Trabectidin 
Ceritinib 
Fuoxetine 
Orlistat 
Trametinib 
Cetuximab 
Fluvastatin 
Oxaliplatin 
Tofacitinib 
Cisplatin 
Fluvoxamine 
Oxaprozin 
Tolcapone 
Cladribine 
Gabapentin 
Paclitaxel 
Tolmetin 
Clofarabine 
Gefitinib 
Palbociclib 
Topiramate 
Clonidine 
Gemcitabine 
Pamidronate 
Topotecan 
Clopidogrel 
Griseofulvin 
Panitumumab 
Torsemide 
Clotrimazole 
Guanfacine 
Panobinostat 
Trastuzumab 
Colchicine 
Hydroxyurea 
Pazopanib 
Trazodone 
Cortisone 
Ibuprofen 
Peg-asparaginase 
Tretinoin 
Crizotinib 
IDArubicin 
Pembrolizumab 
Ursolic acid 
Cyclophosphamide 
Ifosfamide 
Pemetrexed 
Valproic acid 
Cyclosporine 
Imatinib 
Pentostatin 
Valrubicin 
Cytarabine 
Indomethacin 
Phenelzine 
Vandetanib 
Dacarbazine 
Irinotecan 
Piperazine 
Vemurafenib 
Dantrolene 
Ipilimumab 
Piroxicam 
Verapamil 
Dasatinib 
Isotretinoin 
Plerixafor 
VinBLAStine 
DAUNOrubicin 
Ixabepilone 
Pravastatin sodium 
VinCRIStine 
Decitabine 
Ketoprofen 
Prazosin hydrochloride 
Vinorelbine 
Denileukin diftitox 
Ketorolac 
PrednisoLONE 
Vismodegib 
Dexamethasone 
Lansoprazole 
Prochlorperazine 
Vorinostat 
Diazoxide 
Lapatinib 
Propylthiouracil 
Zolendronic acid 
Diclofenac 
 
Rabeprazole sodium 
 

Clinical Protocol NMTRC009 
 
Version 3.0 FINAL 
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Confidential 
Issued 10 January 2017  
Naturopathic Drug Table: 
 
 
ALA 
Calcitriol 
Garlic 
Modified citrus pectin 
Ascorbic acid 
Cordyceps 
Ginger (6-gingerol) 
Myrrh (Guggulsterone) 
Astragalus membranaceu s 
Coriolus (versicolor) 
Green Tea 
Pycnogenol 
Berberine 
Curcumin 
Indole-3-Carbinol 
Quercetin 
Black Cumin 
(thymoquinone) 
Fermented wheat germ 
extract 
Lycopene 
Rosemary 
Bromelain 
Frankincense 
Melatonin 
Soy Isoflavones 
 
 
 
Sulforaphane 

Clinical Protocol NMTRC009 
 
Version 3.0 FINAL 
Page 69 of 70 
Confidential 
Issued 10 January 2017  
Appendix IV- Example expression file format for the VCF 4.1: 
 
##fileformat=VCFv4.1 
##DESeq 
##ALT=<ID=EXP,Description="Differential Expression"> 
##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise "> 
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of gene "> 
##INFO=<ID=GENEID,Number=1,Type=String,Description="Ensembl gene ID "> 
##INFO=<ID=GENE,Number=1,Type=String,Description="Common gene symbol "> 
##INFO=<ID=BASEMEAN,Number=1,Type=Float,Description="Average of baseMeanA and 
baseMeanB "> 
##INFO=<ID=BASEMEANA,Number=1,Type=Float,Description="Average normalized counts for 
control sample(s) "> 
##INFO=<ID=BASEMEANB,Number=1,Type=Float,Description="Average normalized counts for 
affected sample(s) "> 
##INFO=<ID=FOLDCHANGE,Number=1,Type=Float,Description="Fold Change (Affected/Control) 
"> 
##INFO=<ID=LOG2FC,Number=1,Type=Float,Description="Log2 Fold Change (Affected/Control) 
"> 
##INFO=<ID=PVALUE,Number=1,Type=Float,Description="p-value "> 
##INFO=<ID=PADJ,Number=1,Type=Float,Description="Multiple hypothesis testing corrected p-
value "> 
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO 
X       99883667        .       N       <EXP>   0.644187137606379       .       
IMPRECISE;END=99894988;GENEID=ENSG00000000003;GENE=TSPAN6;BASEMEAN=3831.61375
995454;BASEMEANA=4951.27397871424;BASEMEANB=2711.95354119485;FOLDCHANGE=0.54
7728433702853;LOG2FC=-
0.868467319327676;PVALUE=0.644187137606379;PADJ=1;REFERENCE=SU2C002_MRN.melano
cyte_control 
 
 

Clinical Protocol NMTRC009 
 
Version 3.0 FINAL 
Page 70 of 70 
Confidential 
Issued 10 January 2017  
Example variant from a VCF file for BRAF V600E mutation: 
7 
140453136 
rs113488022 A 
T 
38.6 PASS 
TYPE=somatic_SNV;DP1=194;DP2=411;AR1=0.010;AR2=0.679;LN=1;PILEUP1=AAAAAaaT
aa 
AaaaAAaAaaaAAaaAaaAAAAaAAaAaAAaAAaAAaaAAaAAaaAAAAAaaaAAAaAaaaAAaAAAAAAAAaA
aA 
aaAAtAaAAAAaaaaAAAAAaAaaaaAaaAAAAAAaAaAAAAAAAaaaAAAAAAaaaAAAAAAaaaaAAaaAaA
aa 
aaaAaAAAAAAAAAAAAaaaAAaAAaaAaaAa;PILEUP2=TTTtaATaaATtTtTttTtttttttttaaAaat
At 
ataTATAttTTTatTttTtTtTATTTtttttatTtATTTTTtTTTAATTtATTtTttTATtTtTAAATtTttTT
Ta 
aTAtaTAtaTTTtATTTtTTAttTTTATAttTATttATATTTattTAATTTtTatATttTTtAAtttAAttTAt
aa 
aaAttAaTttaTTttttAtTtaattATtaaatttATTtTTTttatttTTtTAATtTTtatTaAatAtatTTtAA
Aa 
ttTTaATTAATaAtTTataTtTtttaaattatataTaaattAaTTtTaAtattTtAATATaTTttTTATTtTaT
tA 
AtTaTATtAtAAAtAAAtaAAtTttttatTtatTTtATatTtttTTtatAttTTattAaatttTTatTTATT;M
VC 
1=34.0;MVBQ1=NaN;MVMQ1=60.0;MVC2=34.0;EFF=EXON(MODIFIER|||||BRAF|nonsense_
me 
diated_decay|CODING|ENST00000479537|2|1),NON_SYNONYMOUS_CODING(MODERATE|MI
SS 
ENSE|gTg/gAg|V600E|766|BRAF|protein_coding|CODING|ENST00000288602|15|1), 
ENSE|UTR_ 
3_PRIME(MODIFIER|||||BRAF|nonsense_mediated_decay|CODING|ENST00000497784|1
6| 
1);GENEINFO=BRAF:673;LSD;NSM;OM;OTHERKG;PM;PMC;REF;RSPOS=140453136;RV;S3D;
SA 
O=3;SSR=0;VC=SNV;VP=050268000a01000002110100;WGT=1;dbSNPBuildID=132