Stand Up to Cancer Consortium Genomics-Enabled Medicine for Melanoma (G.E.M.M.): Using Molecularly-Guided Therapy for Patients With BRAF Wild-Type (BRAFwt) Metastatic Melanoma
Phase: PHASE2
Conditions: Recurrent Melanoma, Stage IIIA Melanoma, Stage IIIB Melanoma, Stage IIIC Melanoma, Stage IV Melanoma
Sponsor: Yale University

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Version: 10/21/2016 
 
 Page 2 of 116 
Local Protocol #: HIC#1408014446 
 
 
1.1.11 
26. 
Appendix XIII, 
1.1.11 
174-
175 
Revised interferon diary to correct formatting issue 
27. 
Appendix XIII, 
1.1.12 
179 
Added reference to package insert for paclitaxel 
28. 
Appendix XIII, 
1.1.13 
183 
Added reference to package insert for pemetrexed 
29. 
Appendix XIII, 
1.1.14 
187 
Added reference to package insert for sorafenib 
30. 
Appendix XIII, 
1.1.14 
188-
189 
Revised sorafenib diaries to correct formatting issue 
31. 
Appendix XIII, 
1.1.15 
193 
Added reference to package insert for temozolomide 
32. 
Appendix XIII, 
1.1.15 
194 
Revised temozolomide diary to correct formatting issue 
33. 
Appendix XIII, 
1.1.16 
197 
Added reference to package insert for vorinostat 
34. 
Appendix XIII, 
1.1.16 
198-
199 
Revised vorinostat diaries to correct formatting issue 
35. 
Appendix XIII, 
1.2.1 
216 
Revised alisertib (MLN8237) diary to correct formatting issue 
36. 
Appendix XIII, 
1.2.2 
237-
238 
Revised MLN9708 diaries to correct formatting issue 
37. 
Appendix XIII, 
1.3.1.1 
244 
Revised Interaction with Other Medicinal Products and Other Forms of Interaction section for 
axitinib based on updated Investigator’s Brochure 
38. 
Appendix XIII, 
1.3.1.1 
249-
252 
Revised Expected Adverse Events section for axitinib based on updated Investigator’s 
Brochure and corrected typos in section  
39. 
Appendix XIII, 
1.3.1.1 
252 
Updated pharmaceutical section for axitinib 
40. 
Appendix XIII, 
1.3.1.1 
257-
258 
Revised axitinib diaries to correct formatting issue 
41. 
Appendix XIII, 
1.3.1.1 
259 
Revised Reference section for new axitinib Investigator’s Brochure 
42. 
Appendix XIII, 
1.3.1.2 
262 
Revised exclusion criteria for bosutunib to require Hepatitis B testing and exclude patients with 
a positive Hepatitis B surface antigen (HBsAg) test due to reports of Hepatitis B reactivation in 
patients receiving this class of drugs per updated Investigator’s Brochure 
43. 
Appendix XIII, 
1.3.1.2 
267-
269 
Revised bosutinib expected adverse events based on updated Investigator’s Brochure and 
corrected formatting 
44. 
Appendix XIII, 
1.3.1.2 
270 
Minor changes to bosutinib Pharmaceutical section based on updated Investigator’s Brochure 
45. 
Appendix XIII, 
1.3.1.2 
271 
Added Hepatitis B panel at screening in the bosutinib calendar 
46. 
Appendix XIII, 
1.3.1.2 
274-
275 
Revised bosutinib diaries to correct formatting issue 
47. 
Appendix XIII, 
1.3.1.2 
276 
Revised Reference section with updated bosutinib Investigator’s Brochure version 
48. 
Appendix XIII, 
1.3.1.3 
296-
297 
Revised sunitinib diaries to correct formatting issue 
49. 
Appendix XIII, 
1.3.1.5 
329-
330 
Revised crizotinib diaries to correct formatting issue 
50. 
Appendix XIII, 
1.3.1.6 
332-
349 
Added commercial drug name IBRANCE throughout palbociclib (PD-0332991) appendix as 
Pfizer will be supplying the commercial product 
51. 
Appendix XIII, 
1.3.1.6 
332 
Added reference to the IBRANCE package insert in the Background section for palbociclib 
52. 
Appendix XIII, 
1.3.1.6 
342-
343 
Added fetal harm risk based on IBRANCE (palbociclib) Investigator’s Brochure and package 
insert and corrected typo in palbociclib Expected Advere Event section  
53. 
Appendix XIII, 
1.3.1.6 
344-
345 
Revised palbociclib (PD-0332991, IBRANCE) study calendar to include CBC w/diff on day 15 of 
the first 2 cycles based on IBRANCE package insert recommendations; corrected typo in 
footnote #12 
54. 
Appendix XIII, 
1.3.1.6 
346-
348 
Added additional drug names for PD-0332991 (palbociclib, IBRANCE) in patient diaries and 
reformatted diaries 
55. 
Appendix XIII, 
349 
Added IBRANCE (palbociclib) package insert information to Reference section  

Version: 10/21/2016 
 
 Page 3 of 116 
Local Protocol #: HIC#1408014446 
 
 
1.3.1.6 
56. 
Appendix XIII, 
2.3.2.1 
365-
366 
Revised dacomitinib diaries to correct formatting issue 
57. 
Appendix XIII, 
1.4.1 
377-
378 
Revised pexidartinib (PLX3397) expected adverse events based on safety letter and guidance 
from pharmaceutical company 
58. 
Appendix XIII, 
1.4.1 
382-
383 
Revised pexidartinib (PLX3397) diaries to correct formatting issue 
59. 
Appendix XIII, 
1.5.1 
406-
408 
Revised expected adverse events based on updated Investigator’s Brochure for BGJ398 
60. 
Appendix XIII, 
1.5.1 
408-
409 
Minor revisions to the Pharmaceutical section based on updated BGJ398 Investigator’s 
Brochure 
61. 
Appendix XIII, 
1.5.1 
414-
415 
Revised BGJ398 diaries to correct formatting issue 
62. 
Appendix XIII, 
1.5.1 
416 
Revised Reference section with updated BGJ398 Investigator’s Brochure version 
63. 
Appendix XIII, 
1.6.1 
435-
437 
Revised expected adverse events based on updated MEK162 Investigator’s Brochures 
64. 
Appendix XIII, 
1.6.1 
438 
Minor changes to the MEK162 pharmaceutical text based on updated Investigator’s Brochure 
65. 
Appendix XIII, 
1.6.1 
439 
Adjusted formatting before MEK162 study calendar to remove blank page 
66. 
Appendix XIII, 
1.6.1 
441 
Revised Laboratory Assessment table for MEK162 to match Study Calendar 
67. 
Appendix XIII, 
1.6.1 
443-
444 
Revised MEK162 diaries to correct formatting issue 
68. 
Appendix XIII, 
1.6.1 
445 
Revised Reference section with updated MEK162 Investigator’s Brochure versions 
69. 
Appendix XIII, 
1.7.1 
455-
456 
Revised Potential Drug Interaction section for cabozantinib (XL184) based on updated 
Investigator’s Brochure 
70. 
Appendix XIII, 
1.7.1 
459-
470 
Revised language in Warnings and Precautions and Guidelines for Management of Adverse 
Events section for cabozantinib (XL184) 
71. 
Appendix XIII, 
1.7.1 
477-
480 
Revised Expected Adverse Events section for cabozantinib (XL184) based on updated 
Investigator’s Brochure and guidance from pharmaceutical company 
72. 
Appendix XIII, 
1.7.1 
481 
Revised pharmaceutical section for cabozantinib (XL184) to reflect available strengths as per 
updated Investigator’s Brochure and updated drug product section 
73. 
Appendix XIII, 
1.7.1 
488-
489 
Revised cabozantinib (XL184) patient diaries to allow water (drug to be taken in fasted state but 
water is allowed) per Investigator’s Brochure and revised formatting  
74. 
Appendix XIII, 
1.7.1 
490 
 
Revised Reference section to update Investigator’s Brochure version information  
 
 

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Sample 
Whole Blood for 
Correlative Study (RNA) 
Time points 
All patients: Day of initial biopsy, at the 
time of clinical response (if any) and at 
the time of progression  
Additionally: 
 Patients on 28 day cycle: Cycle 1, Day 
15 (prior to dosing) 
Patients on 21 day cycle: Cycle 2, Day 1 
(prior to dosing) 
No. of  samples 
per time point 
One 2.5 ml PAXgene 
Blood RNA tube 
Process 
 
Collect blood in  one labeled 2.5 
ml PAXgene™  RNA tube. 
 
Immediately after collection, 
invert the tube 8-10 times. 
 
  

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Place tube in -20ºC
freezer for a minimum of 
24 hours then transfer to 
-70ºC/-80ºC for longer storage until 
ready to ship. 
 
 
 
Storage 
condition: 
-70ºC/-80ºC 
 
Shipping 
condition: 
Dry ice 
Ship to: 
BioProcessing Solutions Alliance 
Note: Whole blood for RNA (PAXgene 
blood RNA tube) samples can be stored 
at the site and should be sent in a batch 
shipment when the patient comes off 
study to save on shipping costs. 
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Figure 1.  Schematic showing flow of information to and from the Molecular and Clinical Tumor Boards. 
 
Patient Profile  
The next generation sequencing approaches employed in the Genomics-Enabled Medicine for 
Melanoma study will identify somatic events from normal/tumor pairs at the genomic (DNA) level, 
including coding point mutations and small insertions/deletions, copy number changes, and structural 
events (intra-chromosomal rearrangements and translocations), and at the transcriptomic (RNA) level 
including differential gene expression and RNA fusions.  These aggregate data sets will be curated and 
annotated by the Genome Processing and Knowledge Recovery Team at TGen, and a molecular profile 
will be generated for each patient.  This molecular profile will be collected along with the patient’s 
histopathology information and clinical history to form a patient profile.  As described in more detail 
below, this patient profile will be used to generate a Genomics-Enabled Medicine for Melanoma 
(GEMM) report, which will be shared with the Molecular Tumor Board who will assess the weight of 
genomic evidence in support of particular target/drug matches.  
 
The Study Pharmacopeia 
Investigational agents in the study pharmacopeia were selected under the auspices of the assembled 

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SU2C team under the direction of Dr. Patricia LoRusso.  Selection criteria included: mechanisms of action 
relevant to non-BRAF mutated melanoma biology; previous knowledge of drug and possible preclinical 
and clinical efficacy; prior determination of a recommended Phase 2 dose (RP2D) and/or maximally 
tolerated dose (MTD); and drug availability.  Approved oncology agents were selected from broad 
therapeutic classes based on information available from the Melanoma Disease Model initiative from 
Cancer Commons and the Melanoma Molecular Map Project.  Target/drug matching is performed 
through curation of PubMed biomedical database and publications to identify those molecular events 
that alter drug response. The gene/drug annotation framework is based on the Targeted Therapeutic 
Database maintained by the Melanoma Molecular Map Project.  The supporting evidence comes from a 
variety of sources including PubMed, clinicaltrials.gov, and DrugDex (Thomson Reuters).  While the total 
drug pool available to this study using this approach is currently 326 FDA approved drugs, only those 
that overlap with the drug list being evaluated in this clinical trial will be considered by the Molecular 
and Clinical Tumor Boards. 

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THE Drug KNOWLEDGE Database 
Figure 2.  Drug knowledge base and report 
table. This figure illustrates data types, 
annotation tables and report outputs. The top 
panel is an example of genomic data format to 
be matched against the rules base. The middle 
panel is an example of a rule annotation table 
that holds drug to genomic aberration 
evidence. The bottom panel is an example of 
rule table to present in report to be presented 
to tumor board. 
Figure 2 illustrates the knowledge library 
that will be used in the study to match 
targets to drugs within our pharmacopeia.  
A target/drug knowledge database was 
constructed based on a novel conceptual 
framework and contains defined rules that 
match specific genomic aberrations to 
selected therapeutic options contained 
within the pharmacopeia. The knowledge 
base is structured with a unique data format 
and controlled vocabulary. The knowledge 
base allows for the systematic capture of 
drug to gene response relationships or 
“rules”. The primary annotation source is 
the PubMed database, and publications 
within; however, other sources of 
information are leveraged when 
appropriate. The evidence statement behind the annotated relationships is recorded and unique URL 
referencing the source is also captured.  
The conceptual framework, developed to annotate genomic aberrations to drug response, is unique in 
that it allows for capturing of contextual information other than simple binary gene to drug response 
relationships. Development of rule structure begins with base statement: ‘gene A is target of drug A’. 
This base relationship is then appended with a modifier term that can influence the state of the drug 
target or biomarker. The state of the biomarker implies either activation or inactivation of the target 
gene product. Activation is assumed to suggest efficacy of drug and inactivation would suggest the 
opposite. There are two forms of modifiers, either intrinsic or extrinsic. The intrinsic modifier is an 
inherent property of the biomarker and is defined as the genomic context that influences drug response. 
The genomic context relates to the aberration of the drug target that encompasses DNA 
amplification/deletion, mutation, mRNA under/overexpression or gene fusion. The extrinsic modifier is 
a defined as a gene, with a distinct genomic context, that influences the state of the target gene and 

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drug response. The extrinsic modifier may also directly influence drug response in the absence of the 
drug target.  
Operating within the above defined framework relationships between genes, either biomarkers or 
modifiers, and therapeutic agents, the evidence of the relationship is marked with the indication and 
evidence type. The indication of the relationship is recorded as either ‘yes’ or ‘no’. If the relationship 
between biomarker, extrinsic modifier and drug indicates positive response to the drug, or a sensitive 
context, it is recorded as a ‘yes’. However, if the relationship indicates a negative response to the drug, 
or a resistant context, it is recorded as ‘no’. The evidence type can be of two forms, direct or inferred. 
Direct evidence is recorded when the exact relationship between the biomarker, and if applicable the 
extrinsic modifier, is linked to drug response in the evidence text.  Inferred is used when the relationship 
between the biomarker, and if applicable the extrinsic modifier, is not explicitly linked to drug response 
in the evidence text. This captures instances where a specific genomic event may not be explicitly linked 
to drug response but the gene in question is altered. For example, gene ‘A’ may have a mutation labeled 
‘B’ that is activating; however, only activating mutation ‘C’ in gene ‘A’ has published evidence that it is 
associated with response to drug ‘D’. Mutation ‘B’ in gene ‘A’ will be annotated, but instead of  being 
labeled as “direct”, the label of “inferred” will be applied to that rule statement.  Additionally, inferred 
may be used in cases where the drug may be of the same class and have the same target but is not 
directly linked to the evidence, but there is evidence that links a drug with the same target and genomic 
aberrations to a drug response.  For example, consider developmental drug ‘X’ that targets gene ‘E’. 
There is sparse evidence in the literature concerning genomic events that alter response to that drug. 
However, there exists another drug, ‘drug Y’, that also targets gene ‘E’ by a similar mechanism and has 
multiple observations relating genomic aberrations to response to the drug. This knowledge will be 
annotated in the knowledge base linked to drug ‘X’ with evidence type marked as inferred.  
For example, if PIK3CA is a target, not only might an activating mutation (intrinsic modifier) of 
PIK3CA represent a sensitivity to a PIK3CA targeted drug, but also, PTEN deletion (extrinsic 
modifier), by virtue of its normal interference with PIK3CA’s activity, may represent an activating 
event modifying the net result of PIK3CA’s activity. Another qualifier for building this rule class 
will be based on inferred drug class relations to capture relationships based on similarities of 
drug mechanism. For example, consider drug 'X' that targets PIK3CA kinase activity but does not 
have specific gene information related to altered response in cancer (as in the case of some 
experimental agents on the list). In such a case we apply common knowledge of the PIK3CA 
kinase targeted drug’s response performance for use in regards to this agent. The target of the 
drug, PI3KCA kinase, will serve as the defining drug class definition. These relationships will be 
explicitly marked as based on common knowledge of this mechanistic class of drugs when 
conveyed to the Molecular and Clinical Tumor Boards. 
1.)
Implementation of Knowledge Library 
The drug-rule match algorithm is a mechanistic process operated on the GEMM database that takes as 
inputs genomic aberrations and their values and identifies the drug candidates from the drug rule match 
knowledge base described above. The output consists of records containing both the matched 
biomarkers and drugs with available information in the knowledge base.  In particular, this construct 

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does not restrict the application, and any specific phenotype can be used to match drugs to genomic 
aberrations in any general setting. 
The genomic aberrations are matched to drug rules in the knowledge base using the following criteria: 
x
Match based on the type of genomic aberration of a biomarker with or without exact match of 
the biomarker value 
x
Match based on the type of genomic aberration of a modifier with or without exact match of the 
modifier value 
 
Genomics-Enabled Medicine for Melanoma (GEMM) Report 
Upon execution of the different genomics analytical methodologies and creation of a patient profile, a 
knowledge mining analysis and translational report (termed a “Genomics-Enabled Medicine for 
Melanoma Report”) will be generated for each patient. Each report will provide an interpretation of the 
genomic aberration, an evidence-supported mechanistic explanation to describe the contextual 
vulnerabilities that were found, and a list of recommended FDA-approved drugs and investigational 
therapies in our study drug pharmacopeia relevant to the aberrations. Aberrations are classified 
according to the following criteria: 
4.) Level 1: Published literature links a particular drug to the molecular aberration 
5.) Level 2: Available information (via TCGA, Sanger Cosmic, etc.) indicates a particular aberration in 
molecular profile is thought to be involved in cancer, but published literature does not link this 
aberration to a particular drug 
6.) Level 3: All other molecular aberrations 
Level 1 and Level 2 aberrations will be included in the Genomics-Enabled Medicine for Melanoma 
Report listed in alphabetical order and presented in an unbiased, non-prioritized fashion.  The 
interactive Genomics-Enabled Medicine for Melanoma report allows the reviewers to quickly navigate to 
the underlying knowledge and evidence at multiple levels (for example: to attain more information on 
the specific drug, the drug’s putative target(s), clinical trials assessing the predicted drug’s efficacy, and 
other levels of supporting evidence). The report conveys the predicted efficacy of the drugs identified by 
each of the analytical methods and also highlights evidence that supports or refutes the use of the 
predicted drug in the context of the patient’s disease state (e.g., BRAF wild type metastatic melanoma).  
As a result of molecular profiling, there will be three possible scenarios: 
4) The patient is found to have a BRAF V600 mutation in contrast to the prior negative results 
obtained via testing.  If this event occurs, the patient will be removed from the study;  
5) The profiling results in no potential match with any drug available in our pharmacopeia.  In this 
event, the patient will be removed from the study;  
6) The data defines a potential match (or multiple matches) with a targeted therapy that exists in our 
pharmacopeia.  In this scenario, the Genomics-Enabled Medicine for Melanoma report will be 
completed and distributed to the Molecular Tumor Board. 
 

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The Molecular Tumor Board 
The Molecular Tumor Board will assess the molecular profile generated for the individual patient and 
analyze the weight of evidence in support of a proposed target/drug match. The Molecular Tumor Board 
will meet by conference call/WebEx weekly (or as needed) to review the Genomics-Enabled Medicine 
for Melanoma reports. Molecular profiling data will be given to the Molecular Tumor Board members a 
minimum of 48 hours in advance of the meeting.  The Molecular Tumor Board will consist of expert 
members of the team as follows: 
x
Available clinical PIs  
ͻ
Genomics experts involved in sequencing and analysis, knowledge mining, and computational 
and systems biology 
ͻ
Bioinformaticians 
ͻ
Pharmacy representation 
ͻ
Available molecular biologists 
ͻ
Patient advocates 
 
At least one Genomics expert/bioinformatician, one pharmacy representative, one patient advocate, 
and three clinical investigators will be needed for a proper quorum to hold a Molecular Tumor Board 
meeting.  Each Molecular Tumor Board conference call will be recorded in its entirety.  A summary of 
the meeting will be written and presented to the Medical Overseer. 
 
The Clinical Tumor Board 
A final recommended treatment plan will be generated by the Clinical Tumor Board utilizing the 
information contained in the knowledge mining analysis, information contained in the translational 
Genomics-Enabled Medicine for Melanoma report, and relevant patient clinical characteristics (e.g., 
history & physical, prior treatment history, comorbidities, etc.).  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 in the Genomics-Enabled Medicine for 
Melanoma report.  All agents are listed in the current pharmacopoeia we are planning to use in the 
study, but the selected therapy may differ amongst individual patients depending on several factors, 
including results of their unique molecular profiling. Potential drug interactions between the targeted 
agents and the subject’s routine medications and supplements will be considered by the Clinical Tumor 
Board, as well as patient’s clinical characteristics and prior treatment history.  The decision making 
process, including prioritization of treatments, will be based on the following: 
4.) Depth of knowledge for each individual agent and its response in tumors with similar molecular 
signatures including (but not limited to)peer-reviewed published  in vivo data, in vitro data, and 
response profile differential; 
5.) Safety considerations, including (but not limited to) review of the patient’s history & physical, 
prior treatments, concurrent medications, and potential drug/drug interactions; 
6.) Expertise of team in evaluating each target 

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The Clinical Tumor Board will meet by conference call/WebEx bi-weekly or more frequently as needed 
following each Molecular Tumor Board. The Clinical Tumor Board will consist of expert members of the 
team as follows: 
x
At least three study clinical investigators 
ͻ
Additional clinical investigators, as available 
ͻ
At least one patient advocates (non-voting) 
ͻ
At least one pharmacy representative (non-voting) 
The final treatment recommendation will be made through a majority vote of all clinical investigators in 
attendance at the Clinical Tumor Board meeting.  If a majority vote in favor of a specific treatment is not 
reached, discussion will be made whether more information is needed, including the possible 
reconvening of the Molecular Tumor Board, or whether the patient should come off study. In the event 
of an even number of clinical investigators being present on the call, one will be excluded at random 
prior to the vote so that a tie will not occur. 
Representative members of the Clinical Tumor Board also will participate in the Molecular Tumor Board 
and thus be familiar with the discussions that have occurred.  Each Clinical Tumor Board conference call 
will be recorded in its entirety.  A summary of the meeting will be written and presented to the Medical 
Overseer.  If a particular therapy is recommended, a Treatment Plan will be generated and sent to the 
Medical Overseer for review. 
 
Treatment Plan 
Following discussions by the Clinical Tumor Board, the final Treatment Plan will be prepared for the 
review of the Medical Overseer.  This Treatment plan will include (but will not be limited to) the 
following: 
x
Information regarding the drug selected 
x
Summarized patient information as was presented to the Clinical Tumor Board, including 
pertinent relevant clinical characteristics including history & physical, comorbidities, prior 
treatment history, etc. 
x
Summaries from Molecular and Clinical Tumor Board meetings 
Medical Overseer 
The final Clinical & Molecular Tumor Board Treatment Plan will be presented to the independent 
Medical Overseer, who will have the opportunity to reject the purposed regimen requiring reconvening 
of the Clinical Tumor Board.  The independent Medical Overseer will be a board-certified medical 
oncologist with extensive experience in early clinical trials. He/she will review the Tumor Board 
treatment recommendations and supervise trial conduct. The Medical Overseer will ensure that the 
study protocol and procedures were followed in the acquisition and analysis of the patient samples, that 
the drug suggested by the Genomics-Enabled Medicine Inference Report and recommended by the 
Clinical Tumor Board is anticipated to be safe for the patient, and that dose and drug administration 
scheduling are appropriate.  The final treatment regimen, decision of the Medical Overseer, and the 

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summaries of the Molecular and Clinical Tumor Board meetings will be documented. If deemed 
acceptable, the lead clinical site will be notified.   
Treating Physician 
The patient will undergo treatment according to the results of the drug assignment, using the 
appropriate dose and schedule defined by the Clinical Tumor Board and approved by the Medical 
Overseer. The patient will be given the option to proceed with therapy. He/she, must sign a treatment-
specific Consent Memo, which includes a list of known side effects and any additional clinical monitoring 
that may be required or recommended by the FDA, the pharmaceutical company, and/or the Clinical 
Tumor Board.  
Typical for any patient preparing to undergo cancer treatment, during the five-week window when data 
is being generated and analyzed, pretreatment evaluation will occur (e.g., CT scans, blood work, etc). If 
the assigned therapy requires the patient to undergo additional testing specific to a particular drug, it 
will be performed prior to treatment. We fully recognize several scenarios will exist in which a specific 
therapy is assigned but the patient will not be able to undergo that particular treatment, including (but 
not limited to): unique drug-specific inclusion/exclusion restrictions, refusal, physician discretion, co-
morbidities, prior treatments, and unexpected events occurring during the five-week analysis period of 
their tumor. If a patient is unable to receive the assigned treatment due to issues related to eligibility, or 
refuses to receive the recommended treatment, the patient will come off study.