Phase II Study of Clofarabine and High-Dose Melphalan Conditioning Prior to Allogeneic Hematopoietic Cell Transplantation for Myelodysplasia or Acute Leukemia in Remission
Phase: PHASE2
Conditions: Adult Acute Lymphoblastic Leukemia in Remission, Acute Myeloid Leukemia Arising From Previous Myelodysplastic Syndrome, Adult Acute Myeloid Leukemia in Remission, Myelodysplastic Syndrome, Secondary Myelodysplastic Syndrome, Chronic Myelomonocytic Leukemia, Therapy-Related Myelodysplastic Syndrome
Sponsor: City of Hope Medical Center

 
IRB #13130 
 
6/6/17 
Packet: 17 
CITY OF HOPE MEDICAL CENTER 
1500 E. DUARTE ROAD 
DUARTE, CA 91010 
 
DEPARTMENT OF HEMATOLOGY AND HEMATOPOIETIC CELL TRANSPLANTATION 
 
TITLE: PHASE II STUDY OF CLOFARABINE AND HIGH-DOSE MELPHALAN CONDITIONING PRIOR TO 
ALLOGENEIC HEMATOPOIETIC CELL TRANSPLANTATION FOR MYELODYSPLASIA OR ACUTE 
LEUKEMIA IN REMISSION 
 
CITY OF HOPE PROTOCOL NUMBER/VERSION: IRB # 13130   Protocol dated: 06/06/17  
 
 
 
DATE(S)/ OF AMENDMENT(S)/REVISION(S): 
 
Initial Approval 
Protocol Dated 11-26-13 
 
Version 00 
COH Amendment 01 
Title Page Dated 2-3-14 
 
Version 01 
COH Amendment 02  
 
Protocol Dated 4-10-14 
 
 
       
Version 02 
COH Amendment 03  
 
Title Page Dated 06-11-14 
 
 
       
Version 03 
COH Amendment 04  
 
Protocol Dated 08-20-14 
 
 
       
Version 04 
COH Amendment 05  
 
Title Page Dated 09-26-14 
 
 
       
Version 05 
COH Amendment 06  
 
Protocol Dated 10-15-14 
 
 
       
Version 06 
COH Amendment 07  
 
Title Page Dated 12-22-14 
 
 
 
Version 07 
COH Amendment 08   
 
Protocol dated 4-20-15 
 
 
 
Version 08 
COH Amendment 09   
 
Protocol dated 10/6/15 
 
 
 
Version 09 
COH Amendment 10  
 
Title Page Dated 01/07/16 
 
 
 
Version 10 
COH Amendment 11  
 
Protocol dated 06/28/16 
 
 
 
Version 11 
COH Amendment 12  
 
Title Page Dated 11/15/16 
 
 
 
Version 12 
COH Amendment 13  
 
Protocol dated 09/15/16 
 
 
 
Version 13 
COH Amendment 14  
 
Protocol dated 06/06/2017 
 
 
 
Version 14 
COH Amendment 15  
Title Page Revised at Continuation Dated 02/26/2019  
Version 15 
COH Amendment 16  
 
Protocol dated 06/06/2017 (tp)  
 
 
 Packet 16 
COH Amendment 17  
 
Protocol dated 06/06/2017 (tp) 
 
 
 Packet 17 
 
 
 
SITE:  
Bone Marrow 
MODALITY:  
 
 
 
 
IV and oral 
TYPE:  
 
 
 
 
 
Phase II 
 
PRINCIPAL INVESTIGATOR: 
 
 
Monzr Al Malki, M.D. 
 
 
COLLABORATING INVESTIGATOR(S): 
Sandra Thomas, Ph.D., Joycelynne M. Palmer, Ph.D. 
 
PARTICIPATING CLINICIANS: 
Ibrahim Aldoss, M.D., Haris Ali, M.D., Ahmed Aribi, M.D., 
Ji-Lian Cai, M.D., Ph.D., Thai Cao, M.D.,  M.D., Len Farol, 
M.D., Stephen Forman, M.D., Alex Herrera, M.D., Myo 
Htut, M.D.,  Amrita Krishnan, M.D.,  Guido Marcucci, M.D., 
Matthew Mei, M.D., Ryotaro Nakamura, M.D., Nitya 
Nathwani, M.D., Leslie Popplewell, M.D., Vinod Pullarkat, 
M.D.,   Michael Rosenzweig, M.D., Amandeep Salhotra, 
M.D., Tanya Siddiqi, M.D., Eileen Smith, M.D., Ricardo 
Spielberger, M.D., Anthony Stein, M.D., Jasmine Zain, 
M.D., Liana Nikolaenko, M.D.; Karamjeet Sandhu, M.D.  
 
BIOSTATISTICIAN: 
Joycelynne M. Palmer, Ph.D.   

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IRB #13130 
Version 14 
Version Date:  06-06-2017 
 
 
Experimental Design Schema 
Schema 
This single-institution, single-arm phase II trial is designed to evaluate the anti-leukemic activity of the 
clofarabine/melphalan alloHCT conditioning regimen, in patients with acute leukemia in remission or 
high-risk myelodysplasia, as assessed by 2-year progression-free survival (PFS). PFS is defined as time 
from start of protocol treatment to death, disease relapse/progression, or last contact, whichever occurs 
first. 
 
 
*A window of 1-2 days is allowed for stem cell availability  
** The current dose used on this protocol for Melphalan is 100 mg/m² 
Figure 1. Treatment Schema 
 
 
 
 
 
 
 
 
 
 

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IRB #13130 
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Protocol Synopsis 
Protocol Title: 
Phase II study of clofarabine and high-dose melphalan conditioning prior to allogeneic 
hematopoietic cell transplantation for myelodysplasia or acute leukemia in remission 
Brief Protocol Title for the Lay Public (if applicable): 
Phase II study of clofarabine and high-dose melphalan prior to allogeneic hematopoietic cell 
transplantation for treatment of myelodysplasia or acute leukemia in remission 
Study Phase: 
Phase II, with patient safety lead-in 
Participating Sites: 
Single Institution: City of Hope 
Rationale for this Study: 
While allogeneic hematopoietic cell transplantation (alloHCT) is the only option for possible cure 
for many patients with hematological malignancies such as acute leukemia and MDS, many 
patients, especially the older population and younger patients who have been heavily pretreated, 
cannot tolerate full intensity ablative conditioning regimens. Fludarabine and melphalan has been 
efficacious as a reduced intensity conditioning regimen for alloHCT for multiple malignancies, 
but the relapse rate for this regimen remains high. In this study, we are replacing fludarabine with 
clofarabine, a rationally designed second-generation purine nucleoside analog. Since clofarabine 
has increased anti-leukemic activity compared to fludarabine in vitro, and preliminary City of 
Hope data are promising (IRB #06114 – Blood 2012, and IRB #12241 – American Society of 
Hemaology Meeting 2012), we hypothesize that a clofarabine/melphalan conditioning regimen 
for alloHCT in patients with acute leukemia or MDS will yield improved relapse/progression 
rates while maintaining a low-toxicity profile.  
Objectives: 
Primary:  
Following a patient safety lead-in, evaluate the anti-tumor activity of clofarabine given in 
combination with high-dose melphalan as assessed by 2-year progression-free survival (PFS). 
Secondary:  
Estimate overall survival (OS), cumulative incidence (CI) of relapse/progression, and non-relapse 
mortality (NRM) at 100 days, 1 year and 2 years. 
Summarize toxicities/complications by organ and severity, including acute and chronic GVHD, 
and infection. 

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IRB #13130 
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Study Design: 
This is a single-institution, single-arm phase II trial to evaluate the anti-leukemic activity and 
safety/tolerability of the clofarabine/melphalan alloHCT conditioning regimen in patients with 
acute leukemia in remission or high-risk myelodysplasia. A patient safety lead-in will be 
conducted to ensure there are no unexpected toxicities. Ultimately a total of 65 patients will be 
treated and evaluated for progression-free survival at the clofarabine/melphalan dose level 
considered safe as determined during the patient safety lead-in segment of this study. 
The first six patients enrolled on this study will be part of a patient safety lead-in. Initially, a 
group of up to 3 patients can be enrolled. Note: no more than 3 patients can be <30 days post 
stem cell infusion at any time during the patient safety lead-in phase. During the safety lead-in, if 
>1/6 patients experience unacceptable toxicity within 30 days after stem cell infusion, subsequent 
patients will receive a de-escalated dose of melphalan at 100 mg/m2. While not expected, if >1/6 
patients experience unacceptable toxicity at the 40mg/m2 (clofarabine)/100 mg/m2 (melphalan) 
dose level, the clofarabine dose will be reduced to 30mg/m2.  
Endpoints: 
Primary: 
The primary study endpoint is 2-year progression-free survival (PFS). PFS will be estimated 
from the start of treatment to the date of death, disease relapse/progression, or date of last contact 
using the Kaplan-Meier method.  
The primary endpoint for the patient saftey lead-in segment of the study is toxicity. Toxicity will 
be scored on both the Bearman Scale and NCI CTCAE v4.0 Scale. Unacceptable toxicity in a 
given patient is defined as any regimen-related grade III/IV toxicity per Bearman Criteria 
(Appendix B), or for hematologic toxicities, per NCI CTCAE v4.03 toxicity criteria, any grade 4 
neutropenia associated with fever or infection and lasting beyond 3 weeks, or grade 4 neutropenia 
lasting for more than 28 days, or any other regimen-related cause of death. This unacceptable 
toxicity definition was established after reviewing two sources of toxicity data (see protocol 
section 2.1): 1) preliminary data from patients conditioned with clofarabine/melphalan (Forman, 
2013 unpublished) and 2) historical data from patients conditioned with fludarabine/melphalan 
(Forman, 2013 unpublished; Nakamura 2012). Generally, regimen-related grade I/II toxicity per 
Bearman Criteria occurred in >50% of patients, in at least one toxicity class; this was also true for 
hematologic toxicity. Note: The NCI CTCAE v4.0 scale will also be used for reporting of adverse 
events and more detailed reporting.Secondary: 
Secondary study endpoints include: overall survival (OS), cumulative incidence of 
relapse/progression and non-relapse mortality, overall toxicity (Bearman Scale and CTCAE 
v4.0), incidence/severity of acute/chronic GVHD, and infection. 
Sample Size: 
We expect to treat a total of 65 patients in this phase II study; assuming the 40mg/m2 
(clofarabine)/140 mg/m2 (melphalan) dose level is well tolerated.  
With two dose reductions permissible, the overall maximum study sample size could reach 77. 
The first six patients treated will be part of a patient safety lead-in. The safety lead-in will be 
conducted to ensure there are no unexpected toxicities. 

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IRB #13130 
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Estimated Duration of the Study 
10 years: 5 years accrual (23 patients/year), 5 years follow-up after enrolling last patient. 
Summary of Subject Eligibility Criteria: 
Inclusion Criteria: 
 
Ages 18-75 years old 
 
Karnofsky performance status score ≥70. 
 
Patients in 1st or 2nd remission with AML or ALL, who are eligible for stem cell transplant  
– remission defined as no circulating blasts, <5% blasts in the bone marrow, 
normalization of previously detected cytogenetic abnormalities, no 
extramedullary disease 
 
High risk MDS  
– Intermediate II and High risk by IPSS  
– Intermediate, High or Very High by WPSS 
– Transfusion dependent 
– Therapy-related MDS or MDS evolved from previous hematological disorder (excepting 
myelofibrosis)  
 
Patients with CMML are allowed to be enrolled 
 
Patients with MDS that has evolved to AML must be in remission 
 
Patients must not be eligible for fully ablative regimens by the attending physician. 
 
Patients with AML or MDS arising from myeloproliferative neoplasm can be enrolled after 
PI approval on case to case basis, depends on the spleen size and degree of bone marrow 
fibrosis 
 
Bone Marrow should be done within 28 (+ 4 day window) days prior to registration to 
confirm remission.   
 
A pretreatment measured creatinine clearance (absolute value) of ≥ 60 ml/minute. 
 
Patients must have a serum bilirubin ≤2.0 mg/dl, SGOT and SGPT ≤2.5 times the 
institutional upper limits of normal. 
 
Ejection Fraction measured by echocardiogram or MUGA > 50% 
 
DLCO or FEV1 > 45% predicted. 
 
Availability of an HLA matched (6/6) sibling donor or 8/8 matched unrelated donor.   
Donors with mismatch at HLA-A, HLA-B, HLA-C and HLA-DR will be reviewed by 
MUD committee and allowed if their mismatch with the recipient does not require 
additional GVHD prophylaxis (other than Tacrolimus and sirolimus), donors with 
mismatch at HLA-DQ or HLA-DPB are eligible.  Donor evaluation according to COH 
SOP.Donor stem cell source can be either peripheral blood or bone marrow. 
 
All patients must have a psychosocial evaluation prior to transplant as per COH SOP 
 
All subjects must have the ability to understand and the willingness to sign a written 
informed consent. 
 
ALL or AML patients who received chemotherapy (induction or consolidation) can proceed 
to transplant once bone marrow cellularity is >10% with no evidence of leukemia. 
Exclusion Criteria: 
 
Patients who have received a prior autologous or allogeneic transplant are excluded 
 
Patients with suspected or proven CNS leukemia. (Diagnostic lumbar puncture not required 

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before enrollment) 
 
Patients with significant hepatic dysfunction (not meeting LFT eligibility criteria) 
 
Acute promyelocytic leukemia 
 
Patients with myeloproliferative neoplasms  
 
Uncontrolled intercurrent illness including, but not limited to ongoing or active or poorly 
controlled infection, symptomatic congestive heart failure, unstable angina pectoris, cardiac 
arrhythmia, poorly controlled pulmonary disease or psychiatric illness/social situations that 
would limit compliance with study requirements. 
 
Pregnant and lactating women are excluded from this study. 
 
Patients who do not agree to practice effective forms of contraception. 
 
Patients with immune deficiency are at increased risk of lethal infections when treated with 
marrow-suppressive therapy. Therefore, HIV-positive patients are excluded from this 
study. 
 
Patients are excluded if they are Hepatitis B sAg,  Hep B cAb, or Hep C positive.  Patients 
with Hepatitis B cAB positive and Hepatitis B PCR negative are eligible if they started 
prophylactic treatment prior to registration to trial.  
 
Patients who received radiation therapy as part of their leukemia treatment may be 
ineligible and individual cases must be presented to the study PI for eligibility 
determination. 
 
Patients with active 2nd malignancies other than AML, ALL, MDS. Excised skin cancer, 
early stage cervical and prostate cancer allowed. 
 
Any psychiatric, social or compliance issues that, in the treating physician opinion, will 
interfere with completion of the transplant treatment and follow up.  
 
Medical or psychiatric reasons which make the donor unlikely to tolerate or cooperate with 
G-CSF therapy or leukapheresis or bone marrow harvest 
 
Known allergies to clofarabine, melphalan sirolimus or tacrolimus 
 
Cord blood as a donor source is not acceptable. 
Investigational Product Dosage and Administration: 
Clofarabine will be given as an inpatient at 40 mg/m2 IV administration over 2 hours on 5 
successive days (-9 to-5 pre-transplant). If calculated creatinine clearance falls below 50 ml/min, 
subsequent doses of clofarabine in the 5 days of clofarabine treatment will be reduced to 30 
mg/m2 in that patient. If calculated creatinine clearance falls below 30 ml/min, subsequent doses 
of clofarabine will be held and the case will be discussed with the PI. 
Melphalan 100 mg/m2 (current dose) IV will be administered inpatient over 30 minutes on a 
single day (-4 pre-transplant), allow at least 20 hours post last clofarabine dose. On day 0, 
patients will have an infusion of allogeneic stem cells (derived from peripheral blood or bone 
marrow) from HLA-matched related or unrelated donors.  
Graft versus host prophylaxis will be tacrolimus 0.02 mg/kg/d IV, beginning day –3, and 
sirolimus 12 mg oral loading dose on day –3, followed by 4 mg orally as a single morning daily 
dose (target serum level 3-10 ng/ml by HPLC).  
Clinical Observations and Tests to be Performed: 
We will perform standard of care post-transplantation observations and tests as per SOP.  Follow-
up will be twice weekly for the first 100 days post-transplant, twice monthly until 6 months post-
transplant, and monthly until the patient is off immunosuppressive therapy without evidence of 
GVHD. Follow-up will be as clinically indicated through year 5, including bone marrow biopsies 

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on day 30, 100 (all ± 7 days), and 1 year and 2 years (all ± 14 days) post-transplant, with yearly 
follow-up through 5 years including data collection on survival and disease status.  
Statistical Considerations: 
This single-institution, single-arm phase II trial is designed to evaluate the anti-leukemic activity 
(as assessed by 2-year PFS) and safety/tolerability of the clofarabine/melphalan alloHCT 
conditioning regimen in patients with acute leukemia in remission or high-risk myelodysplasia.  
Based on PFS estimates from previously reported studies and COH pilot studies, a total of 65 
patients are required. Using the SWOG, single arm non-parametric approach (based on work 
done by Brookmeyer and Crowley) an increase in two-year PFS from an historical estimate of 
62% to 77% would be detectable with approximately 86% power, 1-sided α=0.05. 
The primary endpoint, PFS, will be calculated using the Kaplan-Meier product-limit method. 
Secondary endpoints include, toxicity, incidence and severity of acute and chronic GVHD, and 
infection. Toxicity will be assessed and reported using the Bearman and CTCAE v4.03 scales. 
The cumulative incidence of acute and chronic GVHD will be estimated after taking into account 
the competing risks of death, relapse/progression, and graft failure. Additional secondary 
endpoints will include overall survivival (OS), cumulative incidence of relapse/progression and 
non-relapse mortaility (NRM). OS will be calculated using the Kaplan-Meier product-limit 
method. The cumulative incidence of relapse/progression and non-relapse mortality will be 
calculated as competing risks using the Gray method.  
Sponsor/Licensee: 
Sanofi-Aventis will provide the clofarabine for the study. 
Case Report Forms 
Medidata Rave® EDC Application 

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Table of Contents 
 
SECTION .............................................................................................................................. PAGE 
Experimental Design Schema .......................................................................................................... 1 
Protocol Synopsis............................................................................................................................. 2 
Table of Contents ............................................................................................................................. 7 
Abbreviations ................................................................................................................................. 10 
1.0 
Goals and Objectives (Scientific Aims) ............................................................................ 13 
2.0 
Background ....................................................................................................................... 13 
2.1 
Introduction/Rationale for Development ............................................................. 13 
2.2 
Overview of Proposed Study ............................................................................... 16 
2.3 
Preclinical Studies ................................................................................................ 16 
2.3.1 
Clofarabine in vitro ................................................................................. 16 
2.3.2 
2.3.2 Clofarabine animal studies ............................................................. 17 
2.4 
Human Studies ..................................................................................................... 17 
2.4.1 
Clofarabine single agent trials ................................................................ 17 
2.4.2 
Trials combining clofarabine with alkylating agents .............................. 17 
3.0 
Patient & Donor Eligibility ............................................................................................... 18 
3.1 
Patient Inclusion Criteria ..................................................................................... 18 
3.1.1 
Diagnoses and Disease Status ................................................................. 18 
3.1.2 
Age Criteria, Performance Status and Life Expectancy ......................... 18 
3.1.3 
Child Bearing Potential ........................................................................... 18 
3.1.4 
Protocol-Specific Criteria ....................................................................... 19 
3.1.5 
Informed Consent/Assent ....................................................................... 19 
3.1.6 
Prior Therapy .......................................................................................... 19 
3.2 
Patient Exclusion Criteria .................................................................................... 19 
3.2.1 
Non-Compliance ..................................................................................... 20 
3.3 
Donor Eligibility Criteria ..................................................................................... 20 
3.4 
Inclusion of Women and Minorities .................................................................... 20 
4.0 
Screening and Registration Procedures............................................................................. 20 
4.1 
Screening Procedures ........................................................................................... 20 
4.2 
Informed Consent ................................................................................................ 21 
4.3 
Registration Requirements/Process ..................................................................... 21 
5.0 
Treatment Program ........................................................................................................... 22 

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5.1 
Treatment Overview ............................................................................................ 22 
5.1.1 
Donor Mobilization and Leukapheresis .................................................. 22 
5.1.2 
Patient Treatment Schedule .................................................................... 22 
5.2 
Planned Duration of Therapy ............................................................................... 23 
5.3 
Criteria for Removal from Treatment .................................................................. 23 
5.4 
Subject Follow-Up ............................................................................................... 23 
5.5 
Supportive Care ................................................................................................... 23 
5.6 
Additional Studies ................................................................................................ 23 
5.6.1 
Laboratory Studies .................................................................................. 23 
6.0 
Dose Delays/Modifications  .............................................................................................. 24 
7.0 
Data and Safety Monitoring, Unanticipated Problems and Adverse Event Reporting ..... 24 
7.1 
Definition of Risk Level ...................................................................................... 24 
7.2 
Monitoring and Personnel Responsible for Monitoring ...................................... 24 
7.3 
Definitions ........................................................................................................... 25 
7.4 
Reporting of Unanticipated Problems and Adverse Events ................................. 26 
7.5 
Additional pharmacovigilance requirements bySanofi (clofarabine supplier) .... 28 
7.5.1 
Definitions .............................................................................................. 28 
7.5.2 
Obligations and responsibilities of the IST/ISS sponsor ........................ 29 
7.5.3 
Sanofi group entity pharmacovigilance contact ...................................... 29 
8.0 
Agent Information and Risks ............................................................................................ 30 
8.1 
Concomitant / Prohibited Drugs .......................................................................... 30 
8.1.1 
Tacrolimus/Sirolimus-interacting: P450 inducers causing decreased blood levels
 
30 
8.1.2 
Tacrolimus/Sirolimus-interacting: P450 inhibitors causing increased blood levels
 
30 
8.1.3 
Vaccination ............................................................................................. 30 
8.2 
Clofarabine (from Clolar® full prescribing information) ..................................... 30 
8.2.1 
Clofarabine Drug Description ................................................................. 30 
8.2.2 
Toxicology .............................................................................................. 30 
8.2.3 
Adverse Reactions .................................................................................. 31 
8.2.4 
Warnings ................................................................................................. 31 
8.2.5 
Pharmacology – Handling, Storage, Dispensing and Disposal ............... 32 
8.3 
Melphalan (from Alkeran® full prescribing information) .................................... 35 
8.3.1 
Melphalan Description ............................................................................ 35 
8.3.2 
Toxicology .............................................................................................. 36 

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8.3.3 
Adverse Reactions .................................................................................. 36 
8.3.4 
Warnings ................................................................................................. 37 
8.3.5 
Pharmacology – Handling, Storage, Dispensing and Disposal ............... 37 
8.4 
Tacrolimus (from Prograf® full prescribing information) .................................... 38 
8.4.1 
Tacrolimus Description ........................................................................... 38 
8.4.2 
Toxicology .............................................................................................. 39 
8.4.3 
Adverse Reactions .................................................................................. 40 
8.4.4 
Warnings ................................................................................................. 40 
8.4.5 
Pharmacology – Handling, Storage, Dispensing and Disposal ............... 40 
8.5 
Sirolimus (from Rapamune® full prescribing information) ................................. 42 
8.5.1 
Sirolimus Description ............................................................................. 42 
8.5.2 
Toxicology .............................................................................................. 42 
8.5.3 
Adverse Reactions .................................................................................. 43 
8.5.4 
Warnings ................................................................................................. 43 
8.5.5 
Pharmacology – Handling, Storage, Dispensing and Disposal ............... 45 
9.0 
Correlative/Special Studies ............................................................................................... 46 
10.0 
Study Calendar .................................................................................................................. 48 
10.1 
Pre-transplant study calendar (Conditioning Phase) ............................................ 48 
10.2 
Post-transplant Study Calendar (Stem Cell Infusion and Follow-up) .................. 49 
11.0 
Data Reporting/Protocol Deviations ................................................................................. 52 
11.1 
Data Reporting ..................................................................................................... 52 
11.1.1 Confidentiality and Storage of Records .................................................. 52 
11.1.2 Subject Consent Form ............................................................................. 52 
11.1.3 Data Collection Forms and Submission Schedule .................................. 52 
11.2 
Protocol Deviations .............................................................................................. 52 
11.2.1 Deviation Policy ..................................................................................... 52 
11.2.2 Reporting of Deviations .......................................................................... 53 
11.2.3 Resolving Disputes ................................................................................. 53 
12.0 
Endpoint Evaluation Criteria/Measurement of Effect....................................................... 53 
12.1 
Primary Endpoints ............................................................................................... 53 
12.1.1 Safety Lead-in Segment .......................................................................... 53 
12.1.2 Overall Trial ............................................................................................ 53 
12.2 
Secondary Endpoints ........................................................................................... 53 
12.2.1 Overall Survival (OS) ............................................................................. 53 
12.2.2 Relapse/Progression (CIR) ..................................................................... 53 

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12.2.3 Non-Relapse Mortality (NRM) ............................................................... 54 
12.2.4 Toxicities and Adverse Events ............................................................... 54 
12.2.5 Acute Graft versus Host Disease (aGVHD) of grades 2-4 and 3-4 ........ 54 
12.2.6 Chronic Graft versus Host Disease (cGVHD) ........................................ 54 
12.2.7 Infection .................................................................................................. 54 
12.3 
Disease Status Assessment .................................................................................. 54 
12.3.1 Complete Remission ............................................................................... 54 
12.3.2 Relapse .................................................................................................... 54 
12.3.3 Disease Persistence /Progression: ........................................................... 55 
12.4 
Study Termination ............................................................................................... 55 
13.0 
Statistical Considerations .................................................................................................. 55 
13.1 
Study Design ........................................................................................................ 55 
13.2 
Patient Safety Lead-in Segment ........................................................................... 55 
13.3 
Stopping Rules for Excessive Toxicity ................................................................ 56 
13.4 
Stopping Rules for Activity ................................................................................. 56 
13.5 
Sample Size.......................................................................................................... 57 
14.0 
Human Subject Issues ....................................................................................................... 57 
14.1 
Institutional Review Board .................................................................................. 57 
14.2 
Recruitment of Subjects ....................................................................................... 58 
14.3 
Advertisements .................................................................................................... 58 
14.4 
Study location and Performance Sites ................................................................. 58 
14.5 
Confidentiality ..................................................................................................... 58 
14.6 
Financial Obligations and Compensation ............................................................ 58 
14.7 
Informed Consent Processes ................................................................................ 58 
15.0 
References ......................................................................................................................... 60 
Appendix A: Karnofsky Performance Status Scale ....................................................................... 63 
Appendix B: Modified Bearman Scale [34] .................................................................................. 64 
Appendix C: Acute GVHD Grading and Staging [36] .................................................................. 65 
Appendix D: Chronic GVHD Scoring [37] ................................................................................... 67 
 
Abbreviations 
Abbreviation 
Meaning 
AE 
Adverse Event 

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ALL 
Acute Lymphoblastic Leukemia 
AML 
Acute Myelogenous Leukemia 
CFR 
Code of Federal Regulations 
COH 
City of Hope 
CR 
Complete Response 
CRA 
Clinical Research Associate 
CRF 
Case Report Form 
CTCAE 
Common Terminology Criteria for Adverse Events 
CTEP 
Cancer Therapy Evaluation Program 
DLT 
DNA 
Dose Limiting Toxicity 
Deoxyribonucleic Acid 
DSMC 
Data Safety Monitoring Committee 
EFS 
Event-free Survival 
FDA 
Food and Drug Administration 
GCP 
Good Clinical Practice 
alloHCT 
Allogeneic Hematopoietic Cell Transplantation 
ICF 
Informed Consent Form 
IDS 
Investigational Drug Services 
IND 
Investigational New Drug  
IRB 
Institutional Review Board 
MDS 
Myelodysplastic Syndrome 
MRD 
Minimal Residual Disease 
MTD 
Maximum Tolerated Dose 
NCI 
NRM 
OS 
National Cancer Institute 
Non-relapse Mortality 
Overall Survival 
PD 
Progressive Disease 
PI 
Principal Investigator 
PMT 
Protocol Monitoring Team 
PR 
Partial Response 

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RIC 
SAE 
Reduced Intensity Conditioning 
Serious Adverse Event 
SD 
Stable Disease 

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1.0 Goals and Objectives (Scientific Aims) 
 
Following a patient safety lead-in, determine the anti-tumor activity of clofarabine given in 
combination with high-dose melphalan as assessed by 2-year progression-free survival (PFS). 
 
Estimate overall survival (OS), cumulative incidence (CI) of relapse/progression and non-relapse 
mortality (NRM) at 100 days, 1 year and 2 years. 
 
Summarize toxicities/complications by organ and severity, including acute and chronic GVHD, 
and infection. 
2.0 Background 
2.1 Introduction/Rationale for Development 
Allogeneic stem cell transplantation remains the only curative treatment modality for hematologic 
malignancies such as acute myelogenous leukemia (AML), acute lymphoblastic leukemia (ALL), and 
myelodysplastic syndrome (MDS) [2-4]. Conditioning regimens for allogeneic transplant serve two 
purposes: 1) maximal immunosuppression, to prevent transplant rejection, and, 2) killing any remaining 
tumor cells. There has been an evolution in conditioning regimens over time, with the recognition that 
immunosuppression may be more important than tumor kill by chemotherapy, given that a critical 
component of allogeneic transplant is the graft versus tumor effect [5, 6]. Thus, the first reduced intensity 
regimens were designed, replacing the toxic alkylating agent cyclophosphamide, with the purine 
nucleoside anti-metabolite, fludarabine, which is a potent immunosuppressant with a substantially milder 
toxicity profile [7]. The success of these reduced intensity regimens in terms of lower toxicity, with 
apparently equal efficacy, at least in the case of chronic myelogenous leukemia (CML) and AML in 
patients over age 50 [8], has 
allowed 
the 
benefits 
of 
transplantation to be extended to 
groups 
that 
were 
previously 
excluded [9-11]. Some of the 
most common reduced intensity 
regimens combine fludarabine 
with an alkylating agent, either 
busulfan or melphalan. However, 
fludarabine is not an active agent 
against leukemias or MDS; hence 
it may be beneficial to devise a 
reduced intensity regimen with 
greater anti-tumor efficacy.  
Clofarabine is a rationally designed second-generation purine nucleoside analog, and a relative of 
fludarabine. The double halogen replacement strategy confers resistance to adenosine deaminase, while 
increasing acid stability and bioavailability (in part through more rapid membrane transport) [12]. Figure 
2 diagrams the cellular mechanism of action. Clofarabine enters cells by both facilitated and passive 
diffusion. Initially, deoxycytidine kinase (dCK) phosphorylates clofarabine, after which additional 
kinases phosphorylate it to its active form, clofarabine triphosphate. The triphsophate form acts to 
terminate DNA chain elongation and inhibit repair through incorporation into the DNA chain by 
competitive inhibition of DNA polymerases [13]. It also inhibits ribonucleotide reductase resulting in 
reduction of dNTP pools [14], and induces apoptosis both directly and indirectly via mitochondrial 
damage leading to release of cytochrome c and apoptosis-inducing factor [15]. Clofarabine is more 
efficient than fludarabine at disrupting mitochondrial function, which explains the increased killing of 
Figure 2. Chemical structures of fludarabine phosphate and clofarabine 

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non-dividing lymphocytes by clofarabine compared to fludarabine. This advantage would theoretically 
reduce the likelihood of graft rejection in the allogeneic setting, and perhaps augment the graft-versus-
tumor effect of the donor graft.  
At City of Hope, Kirschbaum et al. performed a phase I study of the combination of clofarabine plus 
melphalan as a reduced intensity conditioning regimen for allogeneic hematopoietic stem cell transplant 
(alloHCT) in patients with acute myelogenous leukemia [16]. Patients over age 18 in complete remission 
or with active disease (up to 50% marrow blasts) who had matched-related or -unrelated donors were 
eligible. The conditioning regimen consisted of escalating doses of clofarabine plus melphalan, followed 
by allogeneic stem cell transplantation. Sixteen patients, with a median age of 63 years, were treated at 
three dose levels; 4 were primary induction failures and 3 were in first relapse. One patient at dose level 2 
and one at dose level 3 died of multi-organ failure; otherwise no dose limiting toxicities were seen. All 
other patients at both doses of clofarabine studied showed complete engraftment by day 30, with a median 
time to absolute neutrophil count recovery of 14 days, and 16 days for platelet recovery. With a median 
follow-up of 17 months, only two patients relapsed and four patients died. Twelve patients were treated at 
dose level 2 (40 mg/m2 clofarabine and 100mg/m2 melphalan) with a 1-year OS of 73% (95% CI 38%-
91%) and EFS of 61% (95% CI 26%-84%). Clofarabine plus melphalan at dose level 2 is a well-tolerated 
conditioning regimen with activity in advanced AML patients. Dose level 3 in the phase I trial treated 
only one patient with co-morbid conditions, who died on day 12 post-transplant from multi-organ failure. 
Since normal engraftment had been achieved at dose level 2, the higher of the tested clofarabine doses, 
further patients were not accrued at dose level three to avoid possible further toxicity.  
Van Besien et al. [17] recently published a phase I/II trial of clofarabine, melphalan, and 
alemtuzumab as conditioning for alloHCT in patients with advanced hematologic malignancies. In the 
Figure 3. Schematic of clofarabine mechanism of action. Borrowed from Bonate et al. [1] 

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phase I portion of the trial, clofarabine 40 mg/m2 with melphalan 140 mg/m2 and alemtuzumab 20 mg 
was found to be safe and tolerable with no DLTs in 6 patients, and this dosing was carried forward into 
the phase II portion. With a median follow-up of 25 months, the 1-yr OS was 59% and 1-yr EFS was45% 
for phase II patients. During the phase II trial they encountered problems with rapid-onset renal failure, 
observing grade 3-5 renal toxicity in 16 of 74 patients during the clofarabine treatment, typically starting 
prior to the melphalan dose. After the first 24 patients, they dose-reduced clofarabine to 30 mg/m2, and 
when the problem continued in the next 27 patients, they increased the clofarabine infusion time from 30 
minutes to 3 hours. Neither of these adjustments decreased the rate of renal toxicity. Other studies using 
clofarabine as transplant conditioning with busulfan [18, 19], and our own phase I study have not seen 
high rates of renal toxicity. Renal complications in the van Besien trial may be particularly related to the 
co-administration of alemtuzumab and clofarabine, which were given on the same days. Elderly patients 
and those with impaired baseline renal function were at higher risk for this complication. We do not 
expect to see an elevated rate of renal toxicity, particularly since the proposed trial will be in less 
advanced patients with fewer pre-treatments and we are requiring a baseline creatinine clearance of ≥ 60 
ml/minute compared to the allowed 50 ml/minute in the van Besien trial.  
Since publication of the Van Besien trial, City of Hope has treated 9 additional patients using 
clofarabine 40 mg/m2 and melphalan 140 mg/m2 dosing (dose level 3 in phase I trial) with no grade 3 
renal toxicity. We have retrospectively analyzed survival outcomes for all 24 COH patients transplanted 
using the clofarabine plus melphalan regimen as their first transplant between November 2007 and 
October 2012. The median follow-up for surviving patients was 23.9 months (range 3.2–52.9). Overall 
survival at 1 year and 2 years was 83.9% and 76.9% respectively, as depicted in Figure 4. Progression-
free survival at 1 and 2 years was the 
same, at 77.7% (95% CI: 57.7 – 89.1). 
The cumulative incidence of acute 
GvHD was 38% (grades I and II only), 
while 
50% 
of 
evaluable 
patients 
experienced chronic GVHD.  
Use 
of 
clofarabine 
in 
place 
of 
fludarabine in the reduced intensity 
conditioning 
regimen 
may 
provide 
enhanced immunosuppression as well as 
a probable increased anti-leukemic 
effect.  For this reason, we propose a 
phase II study of clofarabine combined 
with high-dose melphalan followed by 
allogeneic stem cell reinfusion on day 0. 
As noted, published historical estimates of 2-year PFS post RIC alloHCT vary from 31% to 65%. For 
AML patients who underwent RIC alloHCT in complete remission, using various RIC regimens, 
McClune et al. reported 2-year PFS estimates that ranged from 31%-43%, across four age-groups [20]. 
Marks et al. reported 2-year PFS estimates ranging from 46% (2CR) to 57% (1CR), among ALL patients 
who were also treated with various RIC alloHCT regimens [21]. For high-risk MDS patients treated with 
a fludarabine/melphalan RIC regimen, Nakamura et al. reported a 2-year PFS estimate of 65.2% [22]. 
Because the available historical data for AML and ALL are not reflective of our observed RIC 
fludarabine-melphalan experience (COH PFS estimates are better), 2-year PFS estimates were also 
generated using data from the COH transplant repository from patients transplanted from 2005 to 2009 
using patient selection criteria that match the protocol inclusion criteria. The estimates from these 
analyses are as follows: AML 2-year PFS 60%, ALL 2-year PFS 51% (Forman, 2013 unpublished). 
Using these data, the published MDS outcomes (Nakamura et al. [22]) and expected accrual pattern 
Figure 4. OS and PFS estimates for 24 patients treated with 
Clo/Mel conditioning with a median follow-up time of 24 months.  

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across disease subgroups, the 2-year PFS estimate for fludarabine/melphalan is 62% (95%CI: 57.7-66.5) 
(Figure 5). 
Survival Probability
0.0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1.0
Time (Years) from Date of Transplant
0
1
2
3
4
5
6
7
8
Conditioning Regimens
Clo/Mel (n= 24)
Flu/Mel (n=180)
 
 
2.2 Overview of Proposed Study 
We will be examining the safety and clinical activity of a reduced-intensity conditioning regimen of 
clofarabine and melphalan prior to alloHCT for adult patients with myelodysplastic syndrome, and those 
with acute myelogenous leukemia or acute lymphoblastic leukemia in remission. The primary endpoint 
for this phase II trial is 2-year progression-free survival (PFS), estimated from time of start of treatment to 
death, relapse/progression, or last contact.  
This study will be conducted in compliance with the protocol, Good Clinical Practice (GCP) and the 
applicable regulatory requirements. 
2.3 Preclinical Studies 
2.3.1 
Clofarabine in vitro 
Clofarabine is a potent inhibitor of DNA polymerase, exhibiting significant growth inhibition and 
cytotoxic activity in a wide variety of leukemic and solid tumor cell lines, with IC50 values ranging from 
0.028-0.29 µM [23]. Of the 60 human tumor cell lines in the National Cancer Institute’s Developmental 
Therapeutics Program panel, clofarabine potently inhibits the growth of 35 of them (GI50 from <0.001-
0.45µM [1]. Clofarabine is more efficient than fludarabine at disrupting mitochondrial function, which 
leads to apoptosis via recruitment of APAF-1 [15]. This mitochondria-triggered apoptosis explains the 
increased killing of non-dividing lymphocytes by clofarabine compared to fludarabine. Pretreatment of 
chronic lymphocytic leukemia cells with cyclophosphamide, and alkylating agent that activates DNA 
excision repair mechanisms, facilitates the incorporation of nucleoside analogues and increases their 
cytotoxicity [24]; clofarabine produces a cooperative killing effect with cyclophosphamide at a 10-fold 
lower concentration (5 µM) than does fludarabine (50 µM).  
Figure 5. PFS estimates for 24 patients conditioned for RIC alloHCT with Clo/Mel conditioning and 
180 patients with Flu/Mel at City of Hope.  

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2.3.2 
2.3.2 
Clofarabine animal studies 
Clofarabine demonstrates anti-tumor activity in a wide range of human tumor mouse xenografts [23], and 
was dose and schedule dependent in human lung and colon cancer mouse models [25]. Oral, intravenous, 
and intraperitoneal clofarabine administration routes are all effective [1, 26]. With intravenous 
administration in rats, clofarabine is widely distributed in both normal and tumor tissues and accumulates 
in the liver and myocardium [27]. The volume of distribution at steady state (Vdss) is approximately 1.4-
2.6 L/hg in mice, 3.2-3.6 L/kg in rats, and 0.9-1.2 L/Kg in dogs [1]. IV clofarabine displays non-linear 
pharmacokinetics, with three exponential phases of elimination, with half-lives of 0.3, 1.3, and 12.8 
hours; 80% of the dose is eliminated in urine and 10% in feces [27].  
2.4 Human StudiesType equation here. 
2.4.1 
Clofarabine single agent trials 
In the initial phase I study done at MD Anderson, the MTD was established as 40 mg/m2 daily for 5 days, 
with the DLT being hepatotoxicity seen at the 55 mg/m2 dose. This study included all acute leukemias; 
there was an objective response rate of 16% with 2 complete responses (CR), one in a patient with AML 
and one with ALL, and an additional 2 complete responses without platelet recovery (CRp), one each in 
AML and ALL [28]. A phase II study of 62 patients with acute leukemia followed, using the 40 mg/m2 
dose for 5 days [29]. There were 20 CRs, 1 PR, and 9 patients with hematologic improvement. 
Specifically looking at acute leukemias, CR was seen in 13 of the 31 patients with AML, with another 4 
patients showing CRp, for a total overall response rate of 55%. In ALL, one patient out of 12 developed 
CR. The most frequent toxicities seen in those studies were hyperbilirubinemia and transaminitis, 
resolving by day 15 of therapy, as well as rashes, hand-foot syndrome, and mucositis [29]. A phase I/II 
trial of the combination of clofarabine 40 mg/m2 daily (days 2-6) with ara-C 1 gram/m2 daily (days 1-5), 
in 32 patients with relapsed leukemias, reports 7 patients achieving CR, and 5 patients with CRp, all with 
AML; no patients with ALL in this study attained CR [30]. The lower CR rate seen in the AML patients 
in the phase II study versus the phase I study was explained as being possibly due to two factors: the 
phase II study treated a group of patients at lower clofarabine doses during the dose-finding run-in, also, 
fewer patients in the single agent phase II study had short duration remissions or primary refractory 
disease. 
In the pediatric population, a higher dose was tolerated, with an MTD of 52 mg/m2 established. Four 
patients with ALL and one patient with AML achieved CR, with 1 ALL patient and 2 AML patients 
achieving CR, for a total response rate of 32% [31]. Pediatric phase II studies in ALL using the 52 mg/m2 
dose over 5 days patients are reported [32] with a response rate of 30%: 7 CR, 5 CRs without platelet 
recovery, and 6 PR. Responses were durable enough for 9 patients to proceed to transplant. Toxicities in 
these studies were similar to those seen in the adult studies. The agent subsequently received FDA 
approved for the treatment of relapsed or refractory pediatric ALL.  
2.4.2 
Trials combining clofarabine with alkylating agents 
A phase I trial of clofarabine plus cyclophosphamide (Cy) tested the in vitro findings of synergistic 
activity of these two drugs on leukemia cells [33]. Eighteen patients were treated with Cy (200 mg/m2) on 
day 0, escalating doses of clofarabine + cyclophosphamide on day 2. Overall response rates were 50% for 
dose level 1 (20 mg/m2); however, DLTs including prolonged marrow aplasia required de-escalation to 10 
mg/m2, where the response rate was 30%. DNA damage was increased after clofarabine + Cy compared 
to Cy alone as proof of principle. Since the combined regimen has such potent marrow suppression, it is 
well suited to be an alloHCT conditioning regimen.  
Two groups have conducted trials of clofarabine combined with busulfan, another alkylating agent, as 
part of reduced intensity conditioning for alloHCT. Farag et al. [18] treated a total of 15 relapsed and 
refractory acute leukemia patients in a phase I study using a schedule of 0.8 mg/kg every 6 hours on days 
-6 to -3 pre-transplant, with escalating clofarabine (30-60 gm/m2 daily) on days -6 to -2 pre-transplant. 

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MTD was not reached and grade 3/4 non-hematologic toxicities included vomiting (20%), mucositis 
(60%), hand-foot syndrome (7%), acute renal failure (7%), and reversible elevation of liver enzymes 
(67%). One-year EFS was 53% and OS was 60%. Mineishi et al. [19] report on alternative dosing of 
busulfan (once daily at 3.2 mg/kg IV days -5 to -2) combined with escalating clofarabine (20, 30 or 40 
mg/m2 IV on days -6 to -2) in an ongoing phase I/II study in 46 patients with non-remission 
hematological malignancies [19]. Grade 3-4 non-hematological toxicities include transaminitis (50%), 
mucositis (26%), hand-foot syndrome (13%), transient hypoxia (13%), nausea/vomiting (11%), diarrhea 
(11%), hypertension (7%), veno-occlusive disease (4%), hyperbilirubinemia (4%0, hypersensitivity (2%), 
joint pain (2%) and seizure (2%). There was no renal insufficiency and transaminitis resolved to grade 1 
or less within 2 weeks. All patients engrafted. For the 31 AML patients, the median duration of remission 
was 15.4 months and cumulative incidence of relapse was 38% and overall survival was 50%.  
Two groups, including our own have conducted phase I studies of clofarabine combined with the 
alkylating agent melphalan, as conditioning prior to alloHCT; both of these, Kirschbaum et al. [16] and 
van Besien et al. [17] are described in Section 2.1. 
3.0 Patient & Donor Eligibility 
3.1 Patient Inclusion Criteria  
3.1.1 
Diagnoses and Disease Status 
 
Patients in 1st or 2nd remission with AML or ALL, who are eligible for stem cell 
transplant.  Remission defined asno circulating blasts, <5% blasts in the bone marrow, 
normalization of previously detected cytogenetic abnormalities, no extramedullary 
disease 
 
High risk MDS  
• 
Intermediate II and High risk  by IPSS  
• 
Intermediate, High or very high by WPSS 
• 
Transfusion dependent 
• 
Therapy-related MDS or MDS evolved from previous hematological disorder 
(excepting myelofibrosis)  
 
Patients with CMML are allowed to be enrolled 
 
Patients with MDS that has evolved to AML must be in remission 
 
Patients must not be eligible for full ablative regimens by the attending physician. 
 
Patients with AML or MDS arising from myeloproliferative neoplasm can be enrolled 
after PI approval on case to case basis, depends on the spleen size and degree of bone 
marrow fibrosis 
3.1.2 
Age Criteria, Performance Status and Life Expectancy  
Patients must be ages 18-75 years of age with a performance status of ≥70% on the Karnofsky scale 
(Appendix A). Children will not be treated with this regimen until safety and dose have been established 
in adults. 
3.1.3 
Child Bearing Potential 
The effects of allogeneic transplantation on the developing fetus are highly toxic.  For this reason, women 
of child-bearing potential and men must agree to use adequate contraception (hormonal or barrier method 
of birth control or abstinence] prior to study entry and for six months following duration of study 
participation.  Should a woman become pregnant or suspect that she is pregnant while participating on the 
trial, she should inform her treating physician immediately. 

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3.1.4 
Protocol-Specific Criteria 
 
Bone marrow and peripheral blood studies must be available for confirmation of diagnosis. 
Cytogenetics, flow cytometry, and molecular studies (such as Flt-3 status) will be obtained as per 
standard practice. 
 
Bone marrow aspirates/biopsies should be performed within 28 (+ 4 day window) days from 
registration to confirm disease remission status.   
 
A pretreatment measured creatinine clearance (absolute value) of ≥ 60 ml/minute. 
 
Patients must have a serum bilirubin ≤2.0 mg/dl, SGOT and SGPT ≤2.5 times the institutional upper 
limits of normal. 
 
Ejection fraction measured by echocardiogram or MUGA > 50% 
 
DLCO or FEV1 > 45% predicted. 
 
Availability of an HLA matched (6/6) sibling donor or 8/8 matched unrelated donor.   Donors with 
mismatch at HLA-A, HLA-B, HLA-C and HLA-DR will be reviewed by MUD committee and 
allowed if their mismatch with the recipient does not require additional GVHD prophylaxis (other 
than Tacrolimus and sirolimus), donors with mismatch at HLA-DQ or HLA-DPB are eligible.  Donor 
evaluation according to COH SOP. 
 
Donor stem cell source can be either peripheral blood or bone marrow. 
 
All patients must have a psychosocial evaluation prior to transplant as per COH SOP 
3.1.5 
Informed Consent/Assent 
All subjects must have the ability to understand and the willingness to sign a written informed consent. 
3.1.6 
Prior Therapy 
 
ALL or AML patients who received chemotherapy (induction or consolidation) can proceed to 
transplant once bone marrow cellularity is >10% with no evidence of leukemia. 
3.2 Patient Exclusion Criteria 
 
Patients who have received a prior autologous or allogeneic transplant are excluded 
 
Patients with significant hepatic dysfunction (not meeting LFT eligibility criteria in Section 3.1.4) 
 
Patients with MDS evolved into AML that is not in remission 
 
Patients with acute promyeloctyic leukemia 
 
Patients with myeloproliferative neoplasms  
 
Patients with suspected or proven CNS leukemia. (Diagnostic lumbar puncture not required before 
enrollment) 
 
Uncontrolled intercurrent illness including, but not limited to ongoing or active or poorly controlled 
infection, symptomatic congestive heart failure, unstable angina pectoris, cardiac arrhythmia, poorly 
controlled pulmonary disease or psychiatric illness/social situations that would limit compliance with 
study requirements. 
 
Pregnant and lactating women are excluded from this study. 
 
Patients who do not agree to practice effective forms ofcontraception as described in section 3.1.3. 

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 
Patients with immune deficiency are at increased risk of lethal infections when treated with marrow-
suppressive therapy. Therefore, HIV-positive patients are excluded from this study. 
 
Patients are excluded if they are Hepatitis B sAg, Hep B cAb, or Hep C positive.  Patients with 
Hepatitis B cAB positive and Hepatitis B PCR negative are eligible if they started prophylactic 
treatment prior registration to trial. 
 
Patients who have received radiation therapy as part of their leukemia treatment may be ineligible and 
individual cases must be presented to the study PI for determination of eligibility. 
 
Any psychiatric, social or compliance issues that, in the treating physician opinion, will interfere with 
completion of the transplant treatment and follow up.  
 
Medical or psychiatric reasons which make the donor unlikely to tolerate or cooperate with G-CSF 
therapy or leukapheresis or bone marrow harvest 
 
Known allergies to clofarabine, melphalan sirolimus or tacrolimus 
 
Patients with other active malignancies (besides AML, ALL, MDS) requiring treatment or where 
there is concern of progression are ineligible for this study. However, patients with previously treated 
skin cancer, early stage cervical or prostate cancer may be eligible if there is no evidence of residual 
disease. 
 
Cord blood as a donor source is not acceptable. 
3.2.1 
Non-Compliance 
Subjects, who in the opinion of the investigator, may not be able to comply with the safety monitoring 
requirements of the study. 
3.3 Donor Eligibility Criteria 
Donor evaluation and eligibility will be assessed as per current City of Hope SOP. 
3.4 Inclusion of Women and Minorities 
The study is open to anyone regardless of gender or ethnicity.  Efforts will be made to extend the accrual 
to a representative population, but in a trial which plans to accrue approximately 65 subjects (maximum 
77), a balance must be struck between subject safety considerations and limitations on the number of 
individuals exposed to potentially toxic or ineffective treatments on the one hand, and the need to explore 
gender, racial, and ethnic aspects of clinical research on the other.  If differences in outcome that correlate 
to gender, racial, or ethnic identity are noted, accrual may be expanded or additional studies may be 
performed to investigate those differences more fully. 
4.0 Screening and Registration Procedures 
4.1 Screening Procedures 
Diagnostic or laboratory studies performed exclusively to determine eligibility for this trial will be done 
only after obtaining written informed consent.  Studies or procedures that were performed for clinical 
indications within 30 days prior to registration (not exclusively to determine study eligibility) may be 
used for baseline values, even if the studies were done before informed consent was obtained. Patients 
who received chemotherapy, immunotherapy or radiation need at least a 2 week’ washout period prior to 
registration from the last dose of therapy.  See Section 10.0 – Study Calendar for a complete list of 
screening procedures. Lab values required for eligibility are listed in the Patient Eligibility section 3.1.  
Patient screening tests for eligibility will be based on City of Hope Standard of Care transplant work up. 

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4.2 Informed Consent  
The investigational nature and objectives of the trial, the procedures and treatments involved and their 
attendant risks and discomforts, and potential alternative therapies will be carefully explained to the 
subject and a signed informed consent will be obtained.  Documentation of informed consent for 
screening will be maintained in the subject’s research chart and medical record.   
4.3 Registration Requirements/Process 
See Section 10.0 – Study Calendar for a complete list of pre-study tests. 
Registration is to occur within 4 days of the start of conditioning.  
      Registration  
Patients who received chemotherapy , immunotherapy or radiation need at least a 2 week washout period 
prior to registration from the last dose of therapy.  To register a patient, the treating physician should 
contact the protocol nurse or the responsible Clinical Research Coordinator (CRC) in Clinical Trial Office 
(CTO) to complete the eligibility/registration form. The protocol nurse or CRC will contact the Data 
Coordinating Center at the City of Hope (626-256-4673, ext. 64267 or e-mail dcc@coh.org), EMAIL a 
copy of the completed eligibility checklist, required pre-study tests (per protocol – and may include 
laboratory, CT and pathology reports), signed Informed Consent, signed Patients' Bill of Rights and 
HIPAA authorization form to dcc@coh.org. 
 
Registration Process 
 
The patient registration process will be handled by the Department of Clinical Research Information 
Support (CRIS) Data Coordinating Center (DCC) at City of Hope. The steps below are to be taken when 
registering a patient: 
 
The research staff must assure they have the most current and updated version of the protocol 
and informed consent prior to enrolling a patient.  If a question arises, please contact the Data 
Coordinating Center at 626-256-4673 extension 64267 or via email at dcc@coh.org.   
 
The study staff must assure that all pre-study laboratory tests, scans and x-rays have been 
completed prior to registration according to the study calendar 
 
The study staff must assure that the patient has signed an approved informed consent prior to 
registration/randomization, including the Experimental Subject Bill of Rights and appropriate 
HIPAA authorization. 
 
The study staff must confirm that the patient meets all inclusion and exclusion eligibility 
criteria for the protocol.  The eligibility checklist (provided by the COH DCC) must be 
completed in its entirety. 
 
Registration is to occur within 4 days of the start of conditioning. A patient failing to meet all 
protocol requirements may not be registered.   
 
Once a patient is eligible, all the pre-study requirements have been fulfilled, and the informed 
consent obtained, the research nurse or the study coordinator will inform the COH Data 
Coordinating Center at (626) 256-4673, extension 64267; email dcc@coh.org a copy of the 
patient’s signed informed consent, , completed eligibility checklist and corresponding source 
documentation confirming eligibility (including pathology reports, lab reports, x-ray reports, 
etc.). 
 

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The City of Hope Data Coordinating Center will: 
 
Review all materials/source documentation to ensure the patient is eligible.   
 
Ensure the consent form is valid and is signed correctly by all parties.  If additional 
information is needed or should there be any questions, the Data Coordinating Center will 
immediately contact the participating institution and registration will not occur until all issues 
are resolved.   
 
If there are questions regarding exceptions to the eligibility criteria, please contact he study 
Principal Investigator, as well as the COH DCC.  Documentation of IRB approval of 
exception will need to be submitted as well as the COH DCC. 
 
Confirmation of Registration will be emailed to the study staff noting the patient’s study 
number within 24 hours post receipt of a complete eligibility packet. 
 
The COH DCC will call the research nurse or study coordinator and verbally confirm the 
registration (if needed). 
 
If the patient does not receive protocol therapy following registration, the patient’s 
registration on the study may be cancelled.  The COH DCC should be notified of 
cancellations as soon as possible. 
 
5.0 Treatment Program 
5.1 Treatment Overview 
*A window of 1-2 days is allowed for stem cell availability 
**The current dose used on this protocol for Melphalan is 100 mg/m² 
Figure 3. Treatment Schema 
5.1.1 
Donor Mobilization and Leukapheresis 
Donor stem cells will be mobilized and leukapheresed as per current COH SOP. 
5.1.2 
Patient Treatment Schedule 
Clofarabine will be administered in the inpatient setting at 40 mg/m2 IV over 2 hours on 5 successive days 
(-9 to-5 pre-transplant). Prior to each dose of clofarabine, patients will be pre-medicated with 100 mg 
hydrocortisone as an antiemetic and for prevention of capillary leak syndrome. If one or more signs of 
capillary leak syndrome occurs (unexplained hypotension, tachycardia, and/or tachypnea) during infusion 
of clofarabine, administration of clofarabine will be interrupted and the patient will be administered 12 
mg dexamethasone (8 mg/m2 if weight is less than 50 kg). After the patient is free of symptoms, 
clofarabine administration may resume with caution and dexamethasone will be administered at 20 mg IV 

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daily prior to all subsequent doses of clofarabine. If during the course of the 5 days of clofarabine, the 
calculated creatinine clearance falls below 50 ml/min, subsequent doses of clofarabine will be reduced to 
30 mg/m2. 
Melphalan will be administered inpatient at 100 mg/m2 IV administration over 30 minutes on a single day 
(-4 pre-transplant), allow at least 20 hours post last clofarabine dose. Prior to administration of melphalan, 
patients will be pre-medicated with 10 mg IV dexamethasone as part of anti-emetic prophylaxis.  
On day 0, patients will receive an infusion of allogeneic stem cells from an HLA-matched related or 
unrelated donor as per current COH SOP.  
Graft versus host prophylaxis will be with tacrolimus 0.02 mg/kg/d continuous IV, beginning on day –3 
and converting to oral dosing when the patient is able to tolerate and absorb oral medications. Sirolimus 
will be administered at a 12 mg oral loading dose on day –3, followed by 4 mg orally as a single morning 
daily dose. Target serum levels for both tacrolimus and sirolimus are 5-10 ng/ml for each by HPLC. In the 
absence of GVHD, the immunosuppressive taper will be as per COH SOP.  
For a tabular view of the treatment, monitoring, and follow-up schedule, see study calendar in Section 10. 
5.2 Planned Duration of Therapy 
Initial therapy will require ~4 weeks of inpatient treatment during transplantation. A standard schedule of 
follow-up visits for alloHCT will be used with some additional visits for MRD assessment (see Study 
Calendar Section 10.0) with study follow-up extending 5 years beyond the date of stem cell infusion. 
Patients will be co-enrolled in the COH long-term follow-up protocol for allogeneic transplantation 
(protocol #00029). 
5.3 Criteria for Removal from Treatment 
Disease relapse or progression, unacceptable toxicity, non-compliance with protocol 
5.4 Subject Follow-Up 
Follow-up will be at least once weekly for the first 60 days post-transplant, day 100 (+/- 14 days), day 
180 (+/- 28 days), one year (+/- 28 days) and yearly follow-up afterward up to year 5 post-transplant. 
Follow-up will be as clinically indicated through year 5, including bone marrow biopsies on day 30, 100, 
and 1 year and 2 years post-transplant, with yearly follow-up through 5 years including data collection on 
survival and disease status.  
5.5 Supportive Care 
The following supportive care measures will be administered as per City of Hope Standard Operating 
Procedures: 
 
Dietary requirements 
 
Anti-infective prophylaxis for bacterial, viral, fungal and pneumocystis infections as per COH 
transplant SOP.   Exception: to avoid renal toxicity, Bactrim should not be given during the pre-
transplant period but should be administered only during the post transplant period as indicated 
by COH transplant SOP. 
 
Blood product support (including immunoglobulins) 
5.6 Additional Studies 
NA 
5.6.1 
Laboratory Studies 
See Section 10.0 – Study Calendar for a complete list of required laboratory procedures. Studies or 
procedures that were performed for clinical indications within 30 days  prior to registration (not 

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exclusively to determine study eligibility) may be used for baseline values, even if the studies were done 
before informed consent was obtained. Lab values required for eligibility are listed in the Patient 
Eligibility section 3.1.   
6.0 Dose Delays/Modifications  
Patients, with a measured creatinine clearance <100 ml/min at screening, will receive a 25% dose 
reduction of their assigned clofarabine dose. For patients receiving the full planned assigned dose, if 
calculated creatinine clearance falls below 50 ml/min, subsequent doses of clofarabine in the 5 days of 
clofarabine treatment will be reduced by 25%. In either case if the calculated creatinine clearance falls 
below 30 ml/min, subsequent doses of clofarabine will be held and the case will be discussed with the PI. 
7.0 Data and Safety Monitoring  
7.1  Definition of Risk Level 
This is a Risk Level 3 study, as defined in the “City of Hope Data and Safety Monitoring 
Plan”, http://www.coh.org/dsmc/Pages/forms-and-procedures.aspx because it is a phase 
II clinical trial where the risks are at least balanced by the potential benefit to subjects 
and the importance of the knowledge that may result. 
7.2 Monitoring and Personnel Responsible for Monitoring 
The Protocol Management Team (PMT) consisting of the PI, Collaborating Investigator, 
CRA, protocol nurse, and statistician is responsible for monitoring the data and safety of 
this study, including implementation of any stopping rules for safety and efficacy.  
This study will utilize the Phase I tracking log to monitor data and safety for dose 
escalation, recording doses administered, and resultant adverse events in the safety lead-
in segment. The tracking log will contain dose levels administered, DLT-defining adverse 
events, and documentation that the data from a dose level is complete before dose 
escalation. Those data and safety elements will be reported to the COH DSMC as 
applicable within the PMT report, which will be submitted quarterly or semi-annually 
from the anniversary date of activation, as noted in Table 1 below. Protocol specific data 
collection will include the following items: unacceptable toxicity (as defined in Section 
12.1.1), progression-free survival, overall survival (OS), cumulative incidence of 
relapse/progression and non-relapse mortality, overall toxicity (Bearman Scale and 
CTCAE v4.0), incidence/severity of acute/chronic GVHD, and infection. 
Table 1:  City of Hope PMT Reporting Timelines for the DSMC 
 
Risk Level 
Phase 
Standard Reporting Requirement 
RL 1, RL2, and Expanded 
Access Studies 
No reports required 
3 
I 
Every 3 months from activation date, as 
indicated in MIDAS 

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3 
Pilot, 
Feasibility, 
II-IV 
Every 6 months from activation date, as 
indicated in MIDAS 
4 
Pilot, 
Feasibility, 
I-IV 
Every 3 months from activation date, as 
indicated in MIDAS 
 
For the Phase II segment of the study, data and safety will be reported to the COH DSMC 
using the PMT report and submitted according to the timelines in Table 1 above.  
Protocol specific data collection will include the following items: progression-free 
survival, overall survival (OS), cumulative incidence of relapse/progression and non-
relapse mortality, overall toxicity (Bearman Scale and CTCAE v4.0), incidence/severity 
of acute/chronic GVHD, and infection. 
7.3 Definitions 
Adverse event (AE) - An adverse event is any untoward medical experience or change of 
an existing condition that occurs during or after treatment, whether or not it is considered 
to be related to the protocol intervention.  
Unexpected Adverse Event [21 CFR 312.32 (a)] - An adverse event is unexpected if it is 
not listed in the investigator’s brochure and/or package insert; is not listed at the specificity 
or severity that has been observed; is not consistent with the risk information described in 
the protocol and/or consent; is not an expected natural progression of any underlying 
disease, disorder, condition, or predisposed risk factor of the research participant 
experiencing the adverse event. 
 
Expected Adverse Event - Any event that does not meet the criteria for an unexpected 
event OR is an expected natural progression of any underlying disease, disorder, condition, 
or predisposed risk factor of the research participant experiencing the adverse event. 
 
Serious Adverse Event (SAE) [21 CFR 312.32] - defined as any expected or unexpected 
adverse event that results in any of the following outcomes: 
 
Death 
 
Is life-threatening experience (places the subject at immediate risk of death from the 
event as it occurred) 
 
Unplanned hospitalization (equal to or greater than 24 hours) or prolongation of 
existing hospitalization 
 
A persistent or significant disability/incapacity 
 
A congenital anomaly/birth defect 
 
Secondary malignancy 
 
Any other adverse event that, based upon appropriate medical judgment, may 
jeopardize the subject’s health and may require medical or surgical intervention to 
prevent one of the outcomes listed above (examples of such events include allergic 
bronchospasm requiring intensive treatment in the emergency room or at home, blood 
dyscrasias of convulsions that do not result in inpatient hospitalization, or the 
development of drug dependency or drug abuse). 
 

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Unanticipated problem (UP) – Any incident, experience, or outcome that meets all three 
of the following criteria: 
1. Unexpected (in term nature, severity, or frequency) given the following: a) the research 
procedures described in the protocol-related documents such as the IRB approved 
research protocol, informed consent document or Investigator Brochure (IB); and b) the 
characteristics of the subject population being studied; AND 
2. Related or possibly related to participation in the research (possibly related means there 
is a reasonable possibility that the incident, experience, or outcomes may have been 
caused by the drugs, devices or procedures involved in the research); AND 
3. Suggests that the research places subjects or others at greater risk of harm (including 
physical, psychological, economic, or social harm) than previously known or 
recognized. 
4.  
7.4 Reporting of Unanticipated Problems and Adverse Events 
 
Unanticipated Problems - Most unanticipated problems must be reported to the COH DSMC 
and IRB within 5 calendar days according to definitions and guidelines at 
http://www.coh.org/policy/Policies%20and%20Procedures/REVIEWING_AND_REPORTING
_UNANTICIPATED_PROBLEMS.pdf.  Any unanticipated problem that occurs during the 
study conduct will be reported to the DSMC and IRB by submitting electronically in iRIS 
(http://iris.coh.org). 
Serious Adverse Events - All SAEs occurring during this study, whether observed by the 
physician, nurse, or reported by the patient, will be reported according to definitions and 
guidelines at 
http://www.coh.org/policy/Policies%20and%20Procedures/REVIEWING_AND_REPORTING
_UNANTICIPATED_PROBLEMS.pdf and Table 2 below.  Those SAEs that require expedited 
reporting will be submitted electronically in iRIS (http://iris.coh.org). 
Adverse Events - Adverse events will be monitored by the PMT.  Adverse events that do not 
meet the criteria of serious OR are not unanticipated problems will be reported only in the 
protocol continuation reports and PMT report (see Table 2 below). 
Table 2:  City of Hope Adverse Event and Unanticipated Problem Reporting Timelines for the 
DSMC and IRB 
DSMC Risk Level 3 and Risk Level 4 Protocol Reporting Timelines 
Required Reporting Timeframe to the DSMC 
Attribution 
Unexpected 
Expected 
Death while on active treatment or within 30 days of last day of treatment 
Possibly, Probably, Definitely 
5 calendar days 
Unlikely, Unrelated 
Death after 30 days of last active treatment/therapy 
Possibly, Probably, Definitely 
5 calendar days 
No reporting required 
Unlikely, Unrelated 
No reporting required 
No reporting required 
Within 30 days of last active treatment/therapy 

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Required Reporting Timeframe to the DSMC 
Attribution 
Unexpected 
Expected 
  
Grades 3 and 4 AND meeting the definition of “serious” 
Possibly, Probably, Definitely 
5 calendar days 
10 calendar days 
Unlikely, Unrelated 
5 calendar days 
10 calendar days 
 
Grades 1 and 2 AND resulting in “hospitalization” 
Possibly, Probably, Definitely 
10 calendar days 
10 calendar days 
Unlikely, Unrelated 
10 calendar days 
10 calendar days 
After 30 days of last active treatment/therapy 
 
Grades 3 and 4 AND meeting the definition of “serious” 
Possibly, Probably, Definitely 
10 calendar days 
10 calendar days 
Unlikely, Unrelated 
No reporting required 
No reporting required 
 
Grades 1 and 2 AND resulting in “hospitalization” 
Possibly, Probably, Definitely 
10 calendar days 
10 calendar days 
Unlikely, Unrelated 
No reporting required 
No reporting required 
 
DSMC Risk Level 1 and Risk Level 2 Protocol Reporting Timelines 
Required Reporting Timeframe to DSMC 
Attribution 
Unexpected 
Expected 
  
Death while on active treatment or within 30 days of last day 
of treatment 
Possibly, Probably, Definitely 
5 calendar days 
5 calendar days 
Unlikely, Unrelated 
No reporting required 
No reporting required 
  
Death after 30 days of last active treatment/therapy 
Possibly, Probably, Definitely 
5 calendar days 
No reporting required 
Unlikely, Unrelated 
No reporting required 
No reporting required 
  
Grades 3 and 4 AND meeting the definition of “serious” 
Possibly, Probably, Definitely 
5 calendar days 
10 calendar days 
Unlikely, Unrelated 
No reporting required 
No reporting required 
  
Grades 1 and 2 AND resulting in “hospitalization” 
Possibly, Probably, Definitely 
5 calendar days 
10 calendar days 
Unlikely, Unrelated 
No reporting required 
No reporting required 
 
COH IRB Adverse Event Reporting Timelines  

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Required Reporting Timeframe to COH IRB  
Attribution 
Unexpected 
Expected 
 
Death while on active treatment/therapy or within 30 days 
of the last day of active treatment/therapy 
Possibly, Probably, Definitely 
5 calendar days1 
Annual 
Unlikely, Unrelated 
Annual 
Annual 
 
Grades 3 and 4 
Possibly, Probably, Definitely 
5 calendar days1 
Annual 
Unlikely, Unrelated 
Annual  
Annual 
 
Grade 1 and 2 
Possibly, Probably, Definitely 
5 calendar days1 
Annual2 
Unlikely, Unrelated 
Annual2 
Annual2 
1 These events must be reported in the time frame if they meet the definition of an unanticipated problem. 
2 For studies that are not first in human, Phase I and first in pediatric trials, only grades 3-5 must be reported at annual review.  
 
 
 
 
7.5 Additional Pharmacovigilance requirements by Sanofi (clofarabine supplier) 
7.5.1 
Definitions 
Serious adverse event (SAE): any untoward medical occurrence that at any dose:  
 
Results in death, 
 
Is life threatening, (Note: the term “life-threatening” refers to an event/reaction in which the 
patient was at risk of death at the time of the event/reaction; it does not refer to an event/ 
reaction which hypothetically might have caused death if it were more severe), 
 
Requires inpatient hospitalization or results in prolongation of existing hospitalization, 
 
Results in persistent or significant disability/incapacity, 
 
Is a congenital anomaly/birth defect, or 
 
Is a medically important event or reaction. Medical and scientific judgment should be 
exercised in deciding whether other situations should be considered serious, such as 
important medical events that might not be immediately life-threatening or result in death or 
hospitalization, but might jeopardize the patient or might require intervention to prevent one 
of the other outcomes listed in the definition above. 
Related Adverse Event, i.e. Adverse Drug Reaction (ADR): There is a reasonable possibility 
according to the IST/ISS sponsor that the product may have caused the event. 

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Unexpected Adverse Drug Reaction: An adverse reaction, the nature or severity of which is not 
consistent with the applicable product information (e.g., Investigator's Brochure for an unapproved 
investigational medicinal product or package insert/summary of product characteristics for an 
approved product). An expected ADR with a fatal outcome should be considered unexpected unless 
the local/regional product labeling specifically states that the ADR might be associated with a fatal 
outcome. 
AESI: An adverse event of special interest (AESI) is an adverse event (serious or non-serious) of 
scientific and medical concern specific to the Sponsor’s product or program, for which ongoing 
monitoring and rapid communication by the Investigator to the Sponsor may be appropriate. Such events 
may require further investigation in order to characterize and understand them. AESIs may be added or 
removed during a study by protocol amendment. 
7.5.2 
Obligations and responsibilities of the IST/ISS sponsor  
• 
The IST/ISS sponsor warrants that the study will be performed in compliance with all 
applicable local and international laws and regulations, including without limitation ICH 
E6 guidelines for Good Clinical Practices.  
• 
The IST/ISS sponsor shall be responsible for the respect of all obligations required by 
applicable local and international laws and regulations.  
• 
The sponsor shall be responsible for ensuring submission of required expedited and 
periodic reports to the appropriate Health Authority (HA), the Ethics Committee and 
investigators of each country participating in the IST/ISS (based on applicable 
regulations). 
• 
The IST/ISS sponsor is responsible for providing any “Dear Investigator Letter” (DIL) 
for new safety finding received from Sanofi group entity to the investigators and Ethics 
Committee in each country participating in the study. 
• 
The sponsor must report the following information in English to the Sanofi group entity 
Pharmacovigilance contact: 
1. Routine transmission of: Only related SAEs must be transmitted within 1 
working day of the Investigator’s awareness or identification of the event. 
2. Other events or periodic reports (e.g. Development Safety Update Report 
(DSUR)), submitted to Regulatory Authority must be transmitted at the time of 
submission. 
3. Other significant safety issues or findings in a study pertaining to safety of 
product must be transmitted within 1 working day. (e.g., Data Safety Monitoring 
Board recommendations) 
4. The study report of any IST/ISS must contain a section describing safety review 
and conclusion. 
1. 5. The reference safety information to be used by the IST/ISS sponsor for evaluation 
of expectedness of adverse events shall be the current approved product label 
available in the country. 
7.5.3 
Sanofi Group Entity Pharmacovigilance Contact 
IST/ISS Investigators will notify Sanofi via fax or email, attention Sanofi Pharmacovigilance (PV): 
 
Fax: 908-203-7783   

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E-mail:  USPVmailbox@sanofi-aventis.com. 
 
8.0 Agent Information and Risks 
8.1 Concomitant / Prohibited Drugs 
Management of interacting medications, monitoring of whole blood concentrations and appropriate 
dosage adjustments of immunosuppressant drugs (tacrolimus and sirolimus) will be based on COH 
Hematology SOPs for GVHD prophylaxis. 
8.1.1 
Tacrolimus/Sirolimus-interacting: P450 inducers causing 
decreased blood levels  
Rifampin, rifabutin, magnesium-aluminum-hydroxide, caspofungin, carbamazepine, phenobarbital, 
phenytoin, rifapentine, St. John’s Wort (Hypericum perforatum) 
8.1.2 
Tacrolimus/Sirolimus-interacting: P450 inhibitors causing 
increased blood levels 
Grapefruit juice, ketoconazole, itraconazole, posaconazole, erythromycin, telithromycin, clarithromycin, 
voriconazole, telaprevir, nelfinavir, boceprevir, bromocriptione, cimetidine, cisapride, clotrimazole, 
danazol, diltiazem, fluconazole, HIVprotease inhibitors (e.g., ritonavir, indinavir), metoclopramide, 
nicardipine, troleandomycin, verapamil 
Due to extreme interactions with sirolimus, voriconazole is not recommended during sirolimus therapy. 
However, in the event of suspected or documented fungal infection, voriconazole may be used if deemed 
clinically necessary. In such cases, sirolimus dose should be reduced to 10% of the current dose, and 
tacrolimus dose should be reduced to 30- 50% of the current dose. Consulting with the pharmacist is 
highly recommended for immunosuppressant dose adjustment for drug-drug interactions. 
8.1.3 
Vaccination 
Immunosuppressants may affect response to vaccination. Therefore, during treatment with tacrolimus and 
sirolimus vaccination may be less effective. The use of live vaccines should be avoided; live vaccines 
may include, but are not limited to, the following: measles, mumps, rubella, oral polio, BCG, yellow 
fever, varicella, and TY21a typhoid. 
8.2 Clofarabine (from Clolar® full prescribing information) 
8.2.1 
Clofarabine Drug Description 
Clofarabine (Clolar®) Injection is a purine nucleoside metabolic inhibitor indicated for the treatment of 
pediatric patients 1 to 21 years old with relapsed or refractory acute lympho blas tic leukemia after at least 
two prior regimens, which received initial US FDA approval in 2004. Drug structure and mechanism of 
action are detailed in the background section (2.1) of this protocol. 
8.2.2 
Toxicology 
Clofarabine has not been tested for carcinogenic potential.  
Clofarabine showed clastogenic activity in the in vitro mammalian cell chromosome aberration assay 
(CHO cells) and in the in vivo rat micronucleus assay. It did not show evidence of mutagenic activity in 
the bacterial mutation assay (Ames test). 
Studies in mice, rats, and dogs have demonstrated dose-related adverse effects on male reproductive 
organs. Seminiferous tubule and testicular degeneration and atrophy were reported in male mice receiving 

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intraperitoneal (IP) doses of 3 mg/kg/day (9 mg/m2/day, approximately 17% of clinical recommended 
dose on a mg/m2 basis). The testes of rats receiving 25 mg/kg/day (150 mg/m2/day, approximately 3 times 
the recommended clinical dose on a mg/m2 basis) in a 6-month IV study had bilateral degeneration of the 
seminiferous epithelium with retained spermatids and atrophy of interstitial cells. In a 6-month IV dog 
study, cell degeneration of the epididymis and degeneration of the seminiferous epithelium in the testes 
were observed in dogs receiving 0.375 mg/kg/day (7.5 mg/m2/day, approximately 14% of the clinical 
recommended dose on a mg/m2 basis). Ovarian atrophy or degeneration and uterine mucosal apoptosis 
were observed in female mice at 75 mg/kg/day (225 mg/m2/day, approximately 4-fold of recommended 
human dose on a mg/m2 basis), the only dose administered to female mice. The effect on human fertility is 
unknown. 
8.2.3 
Adverse Reactions 
The most common adverse reactions with clofarabine are (≥ 10%): nausea, vomiting, diarrhea, febrile 
neutropenia, headache, rash, pruritus, pyrexia, fatigue, palmar-plantar erythrodysesthesia syndrome, 
anxiety, flushing, and mucosal inflammation, gastrointestinal disorders (such as enterocolitis, neutropenic 
colitis, cecitis and C. difficile colitis). 
 
The least common adverse reactions with clofarabine are (_<10%): Hemorrhage (may be fatal), 
metabolism and nutrition disorders (such as hyponatremia).  Also, skin and subcutaneous tissue disorders 
(such as Stevens-Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN)) may be fatal. 
 
8.2.4 
Warnings 
Hematologic Toxicity 
 
Monitor complete blood counts and platelet counts during 
clofarabine therapy. (5.1) 
Infections 
 
Clofarabine use is likely to increase the risk of infection, 
including severe sepsis, as a result of bone 
marrow suppression. Monitor patients for signs and 
symptoms of infection and treat promptly. (5.2) 
Hyperuricemia (Tumor Lysis) 
 
Take precautions to prevent and monitor patients for signs 
and symptoms of tumor lysis syndrome, as well as signs and 
symptoms of cytokine release. (5.3) 
Systemic Inflammatory Response Syndrome (SIRS) or Capillary Leak Syndrome 
 
Discontinue clofarabine immediately in the event of signs or 
symptoms of SIRS or Capillary Leak Syndrome 
 
SIRS and Capillary Leak Syndrome may occur. Evaluate and 
monitor patients undergoing treatment for signs and 
symptoms of cytokine release. Consider use of steroids. (5.4) 
Hepatic Enzymes 
 
Monitor and discontinue treatment if necessary. (5.5) 
Hepatic/Renal Impairment 

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 
Use with caution in patients with hepatic or renal 
impairment. Monitor hepatic and renal function.  
Use in Pregnancy 
 
Fetal harm can occur when administered to a pregnant 
woman. Women should be advised to 
avoid becoming pregnant when receiving clofarabine 
 
8.2.5 
Pharmacology – Handling, Storage, Dispensing and 
Disposal 
The population pharmacokinetics of clofarabine were studied in 40 pediatric patients aged 2 to 19 years 
(21males/19 females) with relapsed or refractory acute lymphoblastic leukemia (ALL) or acute 
myelogenous leukemia (AML). At the given 52 mg/m2 dose, similar concentrations were obtained over a 
wide range of body surface areas (BSAs). Clofarabine was 47% bound to plasma proteins, predominantly 
to albumin. Based on non-compartmental analysis, systemic clearance and volume of distribution at 
steady-state were 28.8 L/h/m2 and 172 L/m2, respectively. The terminal half-life was 5.2 hours. No 
apparent difference in pharmacokinetics was observed between patients with ALL and AML or between 
males and females. No relationship between clofarabine or clofarabine triphosphate exposure and toxicity 
or response was found in this population. 
Based on 24-hour urine collections in the pediatric studies, 49-60% of the dose is excreted in the urine 
unchanged. In vitro studies using isolated human hepatocytes indicate very limited metabolism (0.2%). 
The pathways of non-hepatic elimination remain unknown. The pharmacokinetics of clofarabine have not 
been evaluated in patients with renal or hepatic dys function. 
Clofarabine (Clolar®) Injection is supplied in single-use flint vials containing 20 mg of clofarabine in 20 
mL of solution. Each box contains one Clolar®vial (NDC 58468-0100-1) or four Clolar®vials (NDC 
58468-0100-2). The 20 mL flint vials contain 20 mL (20 mg) of solution. The pH range of the solution is 
4.5 to 7.5. 
Vials containing undiluted clofarabine should be stored at 25°C (77°F); excursions permitted to 15-30°C 
(59-86°F). 
Diluted admixtures may be stored at room temperature, but must be used within 24 hours of preparation. 
Procedures for proper handling and disposal should be utilized. Handling and disposal of clofarabine 
should conform to guidelines issued for cytotoxic drugs. 
 
8.3 Melphalan (from Evomela® full prescribing information)  
This formulation is currently being used as of this amendment. 
8.3.1 
Melphalan Description 
Melphalan (Evomela®) contains melphalan hydrochloride, an alkylating drug, as the active ingredient.  
The chemical name of melphalan hydrochloride is 4-[bis(2-chloroethyl)amino]-Lphenylalanine 
hydrochloride.  Its molecular formula is C13H18Cl2N2O2 • HCL and the molecular weight is 341.67.  The 
structural formula is: 

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Melphalan hydrochloride is a white to off-white powder, with a melting range of 199°C - 201°C.  It is 
practically insoluble in water, but freely soluble in 1 N HCL and methanol. 
Evomela (melphalan) for injection is supplied as a sterile white to off-white lyophilized powder in a 
single dose vial for intravenous use.  Each vial contains 50 mg melphalan free base equivalent to 56 mg 
melphalan hydrochloride and 2700 mg Betadex Sulfobutyl Ether Sodium, NF.. 
8.3.2 
Toxicology 
Carcinogenesis, Mutagenesis, Impairment of Fertility: Adequate and well-controlled carcinogenicity 
studies have not been conducted in animals. However, intraperitoneal (IP) administration of melphalan in 
rats (5.4 to 10.8 mg/m2) and in mice (2.25 to 4.5 mg/m2) 3 times per week for 6 months followed by 12 
months post-dose observation produced peritoneal sarcoma and lung tumors, respectively. 
Intramuscular administration of melphalan at 6 and 60 mg/m² produced structural aberrations of the 
chromatid and chromosomes in bone marrow cells of Wistar rats. 
 
8.3.3 
Adverse Reactions 
Hematologic: The most common side effect is bone marrow suppression. For patients receiving Evomela 
as part of a conditioning regimen, myeloablation occurs in all patients.  Do not begin the conditioning 
regimen if a stem cell product is not available for rescue.  Monitor complete blood counts, provide 
supportive care for infections, anemia and thrombocytopenia until there is adequate hematopoietic 
recovery. 
For patients receiving Evomela as palliative treatment, if the bone marrow has been compromised by 
prior irradiation, prior chemotherapy or is recovering from chemotherapy, the risk of severe 
myelosuppression with Evomela is increased.  Perform periodic complete blood counts during the course 
of treatment with Evomela.  Provide supportive care for infections, bleeding, and symptomatic anemia. 
 
Gastrointestinal: For patients receiving Evomela as part of a conditioning regimen, nausea, vomiting, 
mucositis, and diarrhea may occur in over 50% of patients.  Use prophylactic antiemetic medication.  
Provide supportive care for nausea, vomiting, diarrhea, and mucositis.  The frequency grade 3 / 4 
mucositis in clinical studies was 13%.  Provide nutritional support and analgesics for patients with severe 
mucositis. 
For patients receiving Evomela as palliative treatment, nausea and vomiting, diarrhea, and oral ulceration 
may occur.  Use prophylactic antiemetics.  Provide supportive care for nausea, vomiting, diarrhea and 
mucositis. 
 

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Hepatotoxicity:  Hepatic disorders ranging from abnormal liver function tests to clinical manifestations 
such as hepatitis and jaundice have been reported after treatment with melphalan.  Hepatic veno-occlusive 
disease has also been reported.  Monitor liver chemistries. 
 
Hypersensitivity: Acute hypersensitivity reactions including anaphylaxis have occurred in approximately 
2% of patients who received an intravenous formulation of melphalan.  Symptoms may include urticarial, 
pruritis, edema, and skin rashes and, in some patients, tachycardia, bronchospasm, dyspnea, and 
hypotension.  Discontinue treatment with Evomela for serious hypersensitivity reactions.  
Secondary Malignancies:  Melphalan has been shown to cause chromatid or chromosome damage in 
humans.  Secondary malignancies such as myeloproliferative syndrome or acute leukemia have been 
reported in multiple myeloma patients treated with melphalan-containing chemotherapy regimens.  The 
potential benefit of Evomela therapy must be considered against the possible risk of the induction of a 
secondary malignancy. 
 
Embryo-Fetal Toxicity:  Based on its mechanism of action, Evomela can cause fetal harm when 
administered to a pregnant woman.  Melphalan is genotoxic, targets actively dividing cells, and was 
embryolethal and teratogenic in rats.  Advise females of reproductive potential to avoid pregnancy during 
and after treatment with Evomela.  If this drug is used during pregnancy or if the patient becomes 
pregnant while taking this drug, advise the patient of potential risk to the fetus. 
 
Infertility:  Melphalan-based chemotherapy regimens have been reported to cause suppression of ovarian 
function in premenopausal women, resulting in persistent amenorrhea in approximately 9% of patients.  
Reversible or irreversible testicular suppression has also been reported. 
 
Miscellaneous: Other reported adverse reactions include diarrhea, nausea, fatigue, hypokalemia, 
vomiting, hypophosphatemia, decreased appetite, pyrexia, constipation, febrile neutropenia, mucosal 
inflammation, dizziness, edema peripheral, stomatitis, abdominal pain, dysgeusia, The most common 
serious adverse reactions were pyrexia, hematochezia, febrile neutropenia, and renal failure. 
 
8.3.4 
Pharmacology – Handling, Storage, Dispensing and 
Disposal 
Evomela is supplied in a single carton containing one (1) vial.  Each 50 mg vial contains a white to off-
white lyophilized powder in single-dose vial for reconstitution (after reconstitution the solution is clear 
and colorless to light yellow).  Each vial contains 50 mg melphalan free base equivalent to 56 mg 
melphalan hydrochloride. 
NDC 68152-109-00:  Individual carton of Evomela 20 mL single-dose vial containing 50 mg melphalan 
free base. 
Store at controlled room temperature 15° to 30°C (59° to 86°F) and protect from light. 
Parenteral drug products should be visually inspected for particulate matter and discoloration prior to 
administration whenever solution and container permit. If either occurs, do not use this product. 
Retain in original carton until use. 
Melphalan is a cytotoxic drug.  Follow special handling and disposal procedures. 

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Preparation and Administration 
Evomela is a cytotoxic drug.  Follow applicable special handling and disposal procedures. 
Evomela is light sensitive.  Retain in original carton until use. 
Do not mix Evomela with other melphalan hydrochloride for injection drug products. 
Reconstitution and Infusion Instructions: 
1.  Use normal saline (0.9% Sodium Chloride Injection, USP) (8.6 mL as directed) to reconstitute 
Evomela and make a 50 mg/10 mL (5 mg/ mL) nominal concentration of melphalan.  The normal saline 
used to reconstitute each vial should appears to be assisted or pulled into the vial by the negative pressure 
(partial vacuum) present in the vial.  Discard any vial (and replace with another vial) if there is no vacuum 
present when reconstituting the vial with normal saline. 
The reconstituted Evomela drug product is stable for 24 hours at refrigerated temperature (5°C) without 
any precipitation due to the high solubility. 
The reconstituted Evomela drug product is stable for 1 hour at room temperature. 
2.  Calculate the required volume of Evomela needed for a patient’s dose and withdraw that volume from 
the vial(s). 
3. Add the required volume of Evomela to the appropriate volume of 0.9% Sodium Chloride Injection, 
USP to a final concentration of 0.45 mg/mL.  The Evomela admixture solution is stable for 4 hours at 
room temperature in addition to the 1 hour following reconstitution. 
4. Infuse over 30 minutes via an injection port or central venous catheter. 
 
Evomela may cause local tissue damage should extravasation occur.  Do not administer by direct injection 
into a peripheral vein.  Administer Evomela by injecting slowly into a fast-running IV infusion via a 
central venous access line. 
Parenteral drug products should be inspected visually for particulate matter and discoloration prior to 
administration, whenever solution and container permit. 
 
8.4 Melphalan (from Alkeran® full prescribing information)  This formulation was used with 
previous patients enrolled prior to this amendment. 
8.4.1 
Melphalan Description 
Melphalan (Alkeran®), also known as L-phenylalanine mustard, phenylalanine mustard, L-PAM, or L-
sarcolysin, is a phenylalanine derivative of nitrogen mustard. Melphalan is a bifunctional alkylating agent 
that is active against selected human neoplastic diseases. It is known chemically as 4-[bis(2-
chloroethyl)amino]-L-phenylalanine. The molecular formula is C13H18Cl2N2O2 and the molecular weight 
is 305.20. The structural formula is: 
 
Melphalan is an alkylating agent of the bischloroethylamine type. As a result, its cytotoxicity appears to 
be related to the extent of its interstrand cross-linking with DNA, probably by binding at the N7 position 
of guanine. Like other bifunctional alkylating agents, it is active against both resting and rapidly dividing 
tumor cells. 

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8.4.2 
Toxicology 
Carcinogenesis: Secondary malignancies, including acute nonlymphocytic leukemia, myeloproliferative 
syndrome, and carcinoma, have been reported in patients with cancer treated with alkylating agents 
(including melphalan). Some patients also received other chemotherapeutic agents or radiation therapy. 
Precise quantitation of the risk of acute leukemia, myeloproliferative syndrome, or carcinoma is not 
possible. Published reports of leukemia in patients who have received melphalan (and other alkylating 
agents) suggest that the risk of leukemogenesis increases with chronicity of treatment and with 
cumulative dose. In one study, the 10-year cumulative risk of developing acute leukemia or 
myeloproliferative syndrome after oral melphalan therapy was 19.5% for cumulative doses ranging from 
730 to 9,652 mg. In this same study, as well as in an additional study, the 10-year cumulative risk of 
developing acute leukemia or myeloproliferative syndrome after oral melphalan therapy was less than 2% 
for cumulative doses under 600 mg. This does not mean that there is a cumulative dose below which there 
is no risk of the induction of secondary malignancy. The potential benefits from melphalan therapy must 
be weighed on an individual basis against the possible risk of the induction of a second malignancy. 
Adequate and well-controlled carcinogenicity studies have not been conducted in animals. However, 
intraperitoneal (IP) administration of melphalan in rats (5.4 to 10.8 mg/m2) and in mice (2.25 to 4.5 
mg/m2) 3 times per week for 6 months followed by 12 months post-dose observation produced peritoneal 
sarcoma and lung tumors, respectively. 
Mutagenesis: Melphalan has been shown to cause chromatid or chromosome damage in humans. 
Intramuscular administration of melphalan at 6 and 60 mg/m2 produced structural aberrations of the 
chromatid and chromosomes in bone marrow cells of Wistar rats. 
Impairment of Fertility: Melphalan causes suppression of ovarian function in premenopausal women, 
resulting in amenorrhea in a significant number of patients. Reversible and irreversible testicular 
suppression have also been reported. 
Pregnancy: Pregnancy Category D. Melphalan may cause fetal harm when administered to a pregnant 
woman. While adequate animal studies have not been conducted with IV melphalan, oral (6 to 18 
mg/m2/day for 10 days) and IP (18 mg/m2) administration in rats was embryolethal and teratogenic. 
Malformations resulting from melphalan included alterations of the brain (underdevelopment, 
deformation, meningocele, and encephalocele) and eye (anophthalmia and microphthalmos), reduction of 
the mandible and tail, as well as hepatocele (exomphaly). There are no adequate and well-controlled 
studies in pregnant women. If this drug is used during pregnancy, or if the patient becomes pregnant 
while taking this drug, the patient should be apprised of the potential hazard to the fetus. Women of 
childbearing potential should be advised to avoid becoming pregnant. 
 
8.4.3 
Adverse Reactions 
Hematologic: The most common side effect is bone marrow suppression. White blood cell count and 
platelet count nadirs usually occur 2 to 3 weeks after treatment, with recovery in 4 to 5 weeks after 
treatment. Irreversible bone marrow failure has been reported. 
Gastrointestinal: Gastrointestinal disturbances such as nausea and vomiting, diarrhea, and oral ulceration 
occur infrequently. Hepatic disorders ranging from abnormal liver function tests to clinical manifestations 
such as hepatitis and jaundice have been reported. Hepatic veno-occlusive disease has been reported. 
Hypersensitivity: Acute hypersensitivity reactions including anaphylaxis were reported in 2.4% of 425 
patients receiving ALKERAN for Injection for myeloma (see WARNINGS). These reactions were 
characterized by urticaria, pruritus, edema, and in some patients, tachycardia, bronchospasm, dyspnea, 
and hypotension. These patients appeared to respond to antihistamine and corticosteroid therapy. If a 

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hypersensitivity reaction occurs, IV or oral melphalan should not be readministered since hypersensitivity 
reactions have also been reported with oral melphalan. 
Miscellaneous: Other reported adverse reactions include skin hypersensitivity, skin ulceration at injection 
site, skin necrosis rarely requiring skin grafting, vasculitis, alopecia, hemolytic anemia, allergic reaction, 
pulmonary fibrosis, and interstitial pneumonitis. 
8.4.4 
Warnings 
As with other nitrogen mustard drugs, excessive dosage will produce marked bone marrow suppression. 
Bone marrow suppression is the most significant toxicity associated with melphalan in most patients. 
Therefore, the following tests should be performed at the start of therapy and prior to each subsequent 
dose of melphalan: platelet count, hemoglobin, white blood cell count, and differential. 
Thrombocytopenia and/or leukopenia are indications to withhold further therapy until the blood counts 
have sufficiently recovered. Frequent blood counts are essential to determine optimal dosage and to avoid 
toxicity. Dose adjustment on the basis of blood counts at the nadir and day of treatment should be 
considered. 
Hypersensitivity reactions including anaphylaxis have occurred in approximately 2% of patients who 
received the IV formulation. These reactions usually occur after multiple courses of treatment. Treatment 
is symptomatic. The infusion should be terminated immediately, followed by the administration of 
volume expanders, pressor agents, corticosteroids, or antihistamines at the discretion of the physician. If a 
hypersensitivity reaction occurs, IV or oral melphalan should not be readministered since hypersensitivity 
reactions have also been reported with oral melphalan. 
Carcinogenesis: Secondary malignancies, including acute nonlymphocytic leukemia, myeloproliferative 
syndrome, and carcinoma, have been reported in patients with cancer treated with alkylating agents 
(including melphalan). See Toxicology Section 8.2.2 for more details. 
Mutagenesis: Melphalan has been shown to cause chromatid or chromosome damage in humans. 
Intramuscular administration of melphalan at 6 and 60 mg/m2 produced structural aberrations of the 
chromatid and chromosomes in bone marrow cells of Wistar rats. 
Impairment of Fertility: Melphalan causes suppression of ovarian function in premenopausal women, 
resulting in amenorrhea in a significant number of patients. Reversible and irreversible testicular 
suppression have also been reported. 
Pregnancy: Pregnancy Category D. Melphalan may cause fetal harm when administered to a pregnant 
woman. See Toxicology Section 8.2.2 for more details. 
8.4.5 
Pharmacology – Handling, Storage, Dispensing and 
Disposal 
The pharmacokinetics of melphalan after IV administration has been extensively studied in adult patients. 
Following injection, drug plasma concentrations declined rapidly in a biexponential manner with 
distribution phase and terminal elimination phase half-lives of approximately 10 and 75 minutes, 
respectively. Estimates of average total body clearance varied among studies, but typical values of 
approximately 7 to 9 mL/min/kg (250 to 325 mL/min/m2) were observed. One study has reported that on 
repeat dosing of 0.5 mg/kg every 6 weeks, the clearance of melphalan decreased from 8.1 mL/min/kg 
after the first course, to 5.5 mL/min/kg after the third course, but did not decrease appreciably after the 
third course. Mean (±SD) peak melphalan plasma concentrations in myeloma patients given IV melphalan 
at doses of 10 or 20 mg/m2 were 1.2 ± 0.4 and 2.8 ± 1.9 mcg/mL, respectively.  
The steady-state volume of distribution of melphalan is 0.5 L/kg. Penetration into cerebrospinal fluid 
(CSF) is low. The extent of melphalan binding to plasma proteins ranges from 60% to 90%. Serum 
albumin is the major binding protein, while 1-acid glycoprotein appears to account for about 20% of the 

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plasma protein binding. Approximately 30% of the drug is (covalently) irreversibly bound to plasma 
proteins. Interactions with immunoglobulins have been found to be negligible. 
Melphalan is eliminated from plasma primarily by chemical hydrolysis to monohydroxymelphalan and 
dihydroxymelphalan. Aside from these hydrolysis products, no other melphalan metabolites have been 
observed in humans. Although the contribution of renal elimination to melphalan clearance appears to be 
low, one study noted an increase in the occurrence of severe leukopenia in patients with elevated BUN 
after 10 weeks of therapy. 
ALKERAN for Injection is supplied in a carton containing one single-use clear glass vial of freeze-dried 
melphalan hydrochloride equivalent to 50 mg melphalan and one 10-mL clear glass vial of sterile diluent 
(NDC 0173-0130-93). 
Store at controlled room temperature 15° to 30°C (59° to 86°F) and protect from light. 
Parenteral drug products should be visually inspected for particulate matter and discoloration prior to 
administration whenever solution and container permit. If either occurs, do not use this product. 
Preparation for Administration/Stability 
1.  ALKERAN for Injection must be reconstituted by rapidly injecting 10 mL of the supplied diluent 
directly into the vial of lyophilized powder using a sterile needle (20-gauge or larger needle diameter) and 
syringe. Immediately shake vial vigorously until a clear solution is obtained. This provides a 5-mg/mL 
solution of melphalan. Rapid addition of the diluents followed by immediate vigorous shaking is 
important for proper dissolution. 
2.  Infuse undiluted over 20 minutes. 
The time between reconstitution/dilution and administration of ALKERAN should be kept to a 
minimum because reconstituted and diluted solutions of ALKERAN are unstable. Over as short a 
time as 30 minutes, a citrate derivative of melphalan has been detected in reconstituted material from the 
reaction of ALKERAN with Sterile Diluent for ALKERAN. Upon further dilution with saline, nearly 1% 
label strength of melphalan hydrolyzes every 10 minutes. 
A precipitate forms if the reconstituted solution is stored at 5C. DO NOT REFRIGERATE THE 
RECONSTITUTED PRODUCT. 
8.5 Tacrolimus (from Prograf® full prescribing information) 
8.5.1 
Tacrolimus Description 
Tacrolimus, a calcineurin inhibitor previously known as FK506, is a macrolide immunosuppressant 
produced by Streptomyces tsukubaensis. Tacrolimus has an empirical formula of C44H69NO12•H2O and a 
formula weight of 822.03. The chemical structure of tacrolimus is: 

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Tacrolimus inhibits T-lymphocyte activation, although the exact mechanism of action is not known. 
Experimental vidence suggests that tacrolimus binds to an intracellular protein, FKBP-12. A complex of 
tacrolimus-FKBP-12, calcium, calmodulin, and calcineurin is then formed and the phosphatase activity of 
calcineurin inhibited. This effect may prevent the dephosphorylation and translocation of nuclear factor of 
activated T-cells (NF-AT), a nuclear component thought to initiate gene transcription for the formation of 
lymphokines (such as interleukin-2, gamma interferon). The net result is the inhibition of T-lymphocyte 
activation (i.e., immunosuppression). 
Tacrolimus prolongs the survival of the host and transplanted graft in animal transplant models of liver, 
kidney, heart, bone marrow, small bowel and pancreas, lung and trachea, skin, cornea, and limb. 
In animals, tacrolimus has been demonstrated to suppress some humoral immunity and, to a greater 
extent, cell-mediated reactions such as allograft rejection, delayed type hypersensitivity, collagen-induced 
arthritis, experimental allergic encephalomyelitis, and graft versus host disease. 
8.5.2 
Toxicology 
Carcinogenicity studies were conducted in male and female rats and mice. In the 80-week mouse study 
and in the 104-week rat study, no relationship of tumor incidence to tacrolimus dosage was found. The 
highest doses used in the mouse and rat studies were 1.2 to 3.3 times (mice) and 4.0 to 10.8 times (rats) 
the clinical dose range of 0.075 to 0.2 mg/kg/day when corrected for body surface area. 
No evidence of genotoxicity was seen in bacterial (Salmonella and E. coli) or mammalian (Chinese 
hamster lung-derived cells) in vitro assays of mutagenicity, the in vitro CHO/HGPRT assay of 
mutagenicity, or in vivo clastogenicity assays performed in mice; tacrolimus did not cause unscheduled 
DNA synthesis in rodent hepatocytes. 
Tacrolimus given orally at 1.0 mg/kg (0.8 to 2.2 times the clinical dose range of 0.075 to 0.2 mg/kg/day 
based on body surface area) to male and female rats, prior to and during mating, as well as to dams during 
gestation and lactation, was associated with embryolethality and adverse effects on female reproduction. 
Effects on female reproductive function (parturition) and embryolethal effects were indicated by a higher 
rate of pre-implantation loss and increased numbers of undelivered and nonviable pups. When given at 
3.2 mg/kg (2.6 to 6.9 times the clinical dose range based on body surface area), tacrolimus was associated 
with maternal and paternal toxicity as well as reproductive toxicity including marked adverse effects on 
estrus cycles, parturition, pup viability, and pup malformations. 

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8.5.3 
Adverse Reactions 
 
Kidney Transplant: The most common adverse reactions ( ≥ 30%) were infection, tremor, 
hypertension, abnormal renal function, constipation, diarrhea, headache, abdominal pain, insomnia, 
nausea, hypomagnesemia, urinary tract infection, hypophosphatemia, peripheral edema, asthenia, 
pain, hyperlipidemia, hyperkalemia, anemia  
 
Liver Transplant: The most common adverse reactions (≥ 40%) were tremor, headache, diarrhea, 
hypertension, nausea, abnormal renal function, abdominal pain, insomnia, paresthesia, anemia, pain, 
fever, asthenia, hyperkalemia, hypomagnesemia, and hyperglycemia  
 
Heart Transplant: The most common adverse reactions ( ≥ 15%) were abnormal renal function, 
hypertension, diabetes mellitus, CMV infection, tremor, hyperglycemia, leukopenia, infection, 
anemia, bronchitis, pericardial effusion, urinary tract infection and hyperlipemia 
8.5.4 
Warnings 
 
Lymphoma and Other Malignancies: Risk of lymphomas, including post transplant 
lymphoproliferative disorder (PLTD); appears related to intensity and duration of use. Avoid 
prolonged exposure to UV light and sunlight. 
 
Serious infections: Increased risk of bacterial, viral, fungal and protozoal infections, including 
opportunistic infections: combination immunosuppression should be used with caution  
 
Polyoma Virus Infections: Serious, sometimes fatal outcomes, including polyoma virus-associated 
nephropathy (PVAN), mostly due to BK virus, and JC virus-associated progressive multifocal 
leukoencephalopathy (PML); consider reducing immunosuppression  
 
Cytomegalovirus (CMV) Infections: Increased risk of CMV viremia and disease; consider reducing 
immunosuppression  
 
New Onset Diabetes After Transplant: Monitor blood glucose  
 
Nephrotoxicity: Acute and/or chronic; reduce the dose; use caution with other nephrotoxic drugs 
 
Neurotoxicity: Risk of Posterior Reversible Encephalopathy Syndrome, monitor for neurologic 
abnormalities; reduce or discontinue tacrolimus and other immunosuppressants  
 
Hyperkalemia: Monitor serum potassium levels. Careful consideration should be given prior to use of 
other agents also associated with hyperkalemia  
 
Hypertension: May require antihypertensive therapy. Monitor relevant drug-drug interactions  
 
Anaphylactic Reactions with IV formulation: Observe patients receiving tacrolimus for signs and 
symptoms of anaphylaxis  
 
Use with Sirolimus:. For GVHD prophylaxix in hematopoietic cell transplant, use with sirolimus may 
increase the risk of thrombotic microangiopathy (TMA) and levels should be monitored carefully 
 
Myocardial Hypertrophy: Consider dosage reduction or discontinuation 
 
Immunizations: Use of live vaccines should be avoided  
 
Pure Red Cell Aplasia: Discontinuation should be considered 
8.5.5 
Pharmacology – Handling, Storage, Dispensing and 
Disposal 
Pharmacokinetic parameters (mean ± SD) of tacrolimus in healthy human volunteers 

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Absorption of tacrolimus from the gastrointestinal tract after oral administration is incomplete and 
variable. The absolute bioavailability of tacrolimus was 17±10% in adult kidney transplant patients 
(N=26), 22±6% in adult liver transplant patients (N=17), 23±9% in adult heart transplant patients (N=11) 
and 18±5% in healthy volunteers (N=16). 
The rate and extent of tacrolimus absorption were greatest under fasted conditions. The presence and 
composition of food decreased both the rate and extent of tacrolimus absorption when administered to 15 
healthy volunteers. The effect was most pronounced with a high-fat meal (848 kcal, 46% fat): mean AUC 
and Cmax were decreased 37% and 77%, respectively; Tmax was lengthened 5-fold. A high-carbohydrate 
meal (668 kcal, 85% carbohydrate) decreased mean AUC and mean Cmax by 28% and 65%, respectively. 
Tacrolimus capsules should be taken consistently every day either with or without food because the 
presence and composition of food decreases the bioavailability of tacrolimus. 
Tacrolimus is extensively metabolized by the mixed-function oxidase system, primarily the cytochrome 
P-450 system (CYP3A). The major metabolite identified in incubations with human liver microsomes is 
13-demethyl tacrolimus. In in vitro studies, a 31-demethyl metabolite has been reported to have the same 
activity as tacrolimus. 
The mean clearance following IV administration of tacrolimus is 0.040, 0.083, and 0.053, and 0.051 
L/hr/kg in healthy volunteers, adult kidney transplant patients, adult liver transplant patients, and adult 
heart transplant patients, respectively. In man, less than 1% of the dose administered is excreted 
unchanged in urine. 
Tacrolimus for IV must be diluted with 0.9% Sodium Chloride Injection or 5% Dextrose Injection to a 
concentration between 0.004 mg/mL and 0.02 mg/mL prior to use. Diluted infusion solution should be 
stored in glass or polyethylene containers and should be discarded after 24 hours. The diluted infusion 
solution should not be stored in a PVC container due to decreased stability and the potential for extraction 
of phthalates. In situations where more dilute solutions are utilized (e.g., pediatric dosing, etc.), PVC-free 
tubing should likewise be used to minimize the potential for significant drug adsorption onto the tubing. 
Parenteral drug products should be inspected visually for particulate matter and discoloration prior to 
administration, whenever solution and container permit. 
Due to the chemical instability of tacrolimus in alkaline media, tacorlimus should not be mixed or co-
infused with solutions of pH 9 or greater (e.g., ganciclovir or acyclovir). 
The initial dose of tacrolimus is 0.02 mg/kg/day by continuous infusion to start on day minus three. The 
orders should stipulate that the tacrolimus infusion should not be interrupted for more than one hour per 
day. When the patient has recovered from the gastrointestinal toxicity of the conditioning regimen and 
can tolerate and absorb oral medications, tacrolimus should be converted to oral formulation. When 
converting patients from IV to oral, the dose conversion ratio is approximately 1:3 (IV:oral) divided into 
2 doses. Oral tacrolimus is supplied in 0.5 and 1 mg capsules and the dose must be rounded to the nearest 
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Tacrolimus dose is adjusted to maintain a whole blood trough plasma concentration of 5 - 10 ng/ml when 
used in combination with sirolimus. Sequentially rising levels (especially if levels are approaching 10 
ng/ml) and the presence of symptoms of toxicity may be indications for dose reduction. Management of 
interacting medications, monitoring of whole blood concentrations and appropriate dosage adjustments of 
immunosuppressant drugs (tacrolimus and sirolimus) will be based on Hematology SOPs for GVHD 
prophylaxis. 
 
8.6 Sirolimus (from Rapamune® full prescribing information) 
8.6.1 
Sirolimus Description 
Rapamune (sirolimus) is an immunosuppressive agent. Sirolimus is a macrocyclic lactone produced by 
Streptomyces hygroscopicus. Its molecular formula is C51H79NO13 and its molecular weight is 914.2. 
The structural formula of sirolimus is illustrated as follows. 
 
Sirolimus inhibits T-lymphocyte activation and proliferation that occurs in response to antigenic and 
cytokine (Interleukin [IL]-2, IL-4, and IL-15) stimulation by a mechanism that is distinct from that of 
other immunosuppressants. Sirolimus also inhibits antibody production. In cells, sirolimus binds to the 
immunophilin, FK Binding Protein-12 (FKBP-12), to generate an immunosuppressive complex. The 
sirolimus:FKBP-12 complex has no effect on calcineurin activity. This complex binds to and inhibits the 
activation of the mammalian Target Of Rapamycin (mTOR), a key regulatory kinase. This inhibition 
suppresses cytokine-driven T-cell proliferation, inhibiting the progression from the G1 to the S phase of 
the cell cycle. 
8.6.2 
Toxicology 
Carcinogenicity studies were conducted in mice and rats. In an 86-week female mouse study at sirolimus 
doses 30 to 120 times higher than the 2 mg daily clinical (adjusted for body surface area), there was a 
statistically significant increase in malignant lymphoma at all dose levels compared with controls. In a 
second mouse study at dosages that were approximately 3 to 16 times the clinical dose (adjusted for body 
surface area), hepatocellular adenoma and carcinoma in males were considered sirolimus-related. In the 
104-week rat study at dosages equal to or lower than the clinical dose of 2 mg daily (adjusted for body 
surface area), there were no significant findings. 

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Sirolimus was not genotoxic in the in vitro bacterial reverse mutation assay, the Chinese hamster ovary 
cell chromosomal aberration assay, the mouse lymphoma cell forward mutation assay, or the in vivo 
mouse micronucleus assay. 
Fertility was diminished slightly in both male and female rats following oral administration of sirolimus 
at doses approximately 10 times or 2 times, respectively, the clinical dose of 2 mg daily (adjusted for 
body surface area). In male rats, atrophy of testes, epididymides, prostate, seminiferous tubules and/or 
reduction in sperm counts were observed. In female rats, reduced size of ovaries and uteri was observed. 
Reduction of sperm count in male rats was reversible upon cessation of dosing in one study. Testicular 
tubular degeneration was also seen in a 4-week intravenous study of sirolimus in monkeys at doses that 
were approximately equal to the clinical dose (adjusted for body surface area). 
8.6.3 
Adverse Reactions 
The most common (> 30%) adverse reactions are: peripheral edema, hypertriglyceridemia, hypertension, 
hypercholesterolemia, creatinine increased, abdominal pain, diarrhea, headache, fever, urinary tract 
infection, anemia, nausea, arthralgia, pain, and thrombocytopenia 
8.6.4 
Warnings 
Increased Susceptibility to Infection and the Possible Development of Lymphoma. Increased susceptibility 
to infection and the possible development of lymphoma and other malignancies, particularly of the skin, 
may result from immunosuppression. The rates of lymphoma/lymphoproliferative disease observed in 
Studies 1 and 2 were 0.7-3.2% (for sirolimus-treated patients) versus 0.6-0.8% (azathioprine and placebo 
control). Oversuppression of the immune system can also increase susceptibility to infection, including 
opportunistic infections such as tuberculosis, fatal infections, and sepsis. Only physicians experienced in 
immunosuppressive therapy and management of organ transplant patients should use sirolimus. Patients 
receiving the drug should be managed in facilities equipped and staffed with adequate laboratory and 
supportive medical resources. The physician responsible for maintenance therapy should have complete 
information requisite for the follow-up of the patient. 
Hypersensitivity Reactions. Hypersensitivity reactions, including anaphylactic/anaphylactoid reactions, 
angioedema, exfoliative dermatitis and hypersensitivity vasculitis, have been associated with the 
administration of sirolimus. 
Angioedema. Sirolimus has been associated with the development of angioedema. The concomitant use of 
sirolimus with other drugs known to cause angioedema, such as ACE-inhibitors, may increase the risk of 
developing angioedema. 
Fluid Accumulation and Wound Healing. There have been reports of impaired or delayed wound healing 
in patients receiving sirolimus, including lymphocele and wound dehiscence. mTor inhibitors such as 
sirolimus have been shown in vitro to inhibit production of certain growth factors that may affect 
angiogenesis, fibroblast proliferation, and vascular permeability. Lymphocele, a known surgical 
complication of renal transplantation, occurred significantly more often in a dose-related fashion in 
patients treated with Rapamune. Appropriate measures should be considered to minimize such 
complications. Patients with a body mass index (BMI) greater than 30 kg/m2 may be at increased risk of 
abnormal wound healing based on data from the medical literature. There have also been reports of fluid 
accumulation, including peripheral edema, lymphedema, pleural effusion and pericardial effusions 
(including hemodynamically significant effusions and tamponade requiring intervention in children and 
adults), in patients receiving sirolimus. 
Hyperlipidemia. Increased serum cholesterol and triglycerides requiring treatment occurred more 
frequently in patients treated with sirolimus compared with azathioprine or placebo controls. There were 
increased incidences of hypercholesterolemia (43-46%) and/or hypertriglyceridemia (45-57%) in patients 
receiving sirolimus compared with placebo controls (each 23%). The risk/benefit should be carefully 

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considered in patients with established hyperlipidemia before initiating an immunosuppressive regimen 
including sirolimus. Any patient who is administered sirolimus should be monitored for hyperlipidemia. 
If detected, interventions such as diet, exercise, and lipid-lowering agents should be initiated as outlined 
by the National Cholesterol Education Program guidelines. In clinical trials, the concomitant 
administration of sirolimus and HMG-CoA reductase inhibitors and/or fibrates appeared to be well-
tolerated. During Rapamune therapy with cyclosporine, patients administered an HMG-CoA reductase 
inhibitor and/or fibrate should be monitored for the possible development of rhabdomyolysis and other 
adverse effects, as described in the respective labeling for these agents.  
Renal Function. Renal function should be closely monitored during the co-administration of sirolimus 
with cyclosporine, because long-term administration of the combination has been associated with 
deterioration of renal function. Patients treated with cyclosporine and sirolimus were noted to have higher 
serum creatinine levels and lower glomerular filtration rates compared with patients treated with 
cyclosporine and placebo or azathioprine controls. The rate of decline in renal function in these studies 
was greater in patients receiving sirolimus and cyclosporine compared with control therapies. Appropriate 
adjustment of the immunosuppressive regimen, including discontinuation of sirolimus and/or 
cyclosporine, should be considered in patients with elevated or increasing serum creatinine levels. In 
patients at low-to-moderate immunologic risk, continuation of combination therapy with cyclosporine 
beyond 4 months following transplantation should only be considered when the benefits outweigh the 
risks of this combination for the individual patients. Caution should be exercised when using agents (e.g., 
aminoglycosides and amphotericin B) that are known to have a deleterious effect on renal function. In 
patients with delayed graft function, sirolimus may delay recovery of renal function. 
Proteinuria. Periodic quantitative monitoring of urinary protein excretion is recommended. In a study 
evaluating conversion from calcineurin inhibitors (CNI) to sirolimus in maintenance renal transplant 
patients 6-120 months post-transplant, increased urinary protein excretion was commonly observed from 
6 through 24 months after conversion to sirolimus compared with CNI continuation. Patients with the 
greatest amount of urinary protein excretion prior to sirolimus conversion were those whose protein 
excretion increased the most after conversion. New onset nephrosis (nephrotic syndrome) was also 
reported as a treatment emergent adverse event in 2.2% of the sirolimus conversion group patients in 
comparison to 0.4% in the CNI continuation group of patients. Nephrotic range proteinuria (defined as 
urinary protein to creatinine ratio > 3.5) was also reported in 9.2% in the sirolimus conversion group of 
patients in comparison to 3.7% in the CNI continuation group of patients. In some patients, reduction in 
the degree of urinary protein excretion was observed for individual patients following discontinuation of 
sirolimus. The safety and efficacy of conversion from calcineurin inhibitors to sirolimus in maintenance 
renal transplant patients have not been established. 
Interstitial Lung Disease. Cases of interstitial lung disease (including pneumonitis, bronchiolitis 
obliterans organizing pneumonia [BOOP], and pulmonary fibrosis), some fatal, with no identified 
infectious etiology have occurred in patients receiving immunosuppressive regimens including sirolimus. 
In some cases, the interstitial lung disease has resolved upon discontinuation or dose reduction of 
sirolimus. The risk may be increased as the trough sirolimus concentration increases. 
Increased Risk of Calcineurin Inhibitor-Induced Hemolytic Uremic Syndrome/Thrombotic 
Thrombocytopenic Purpura/Thrombotic Microangiopathy (HUS/TTP/TMA). The concomitant use of 
sirolimus with a calcineurin inhibitor may increase the risk of calcineurin inhibitor-induced hemolytic 
uremic syndrome/thrombotic thrombocytopenic purpura/thrombotic microangiopathy (HUS/TTP/TMA). 
Antimicrobial Prophylaxis. Cases of Pneumocystis carinii pneumonia have been reported in patients not 
receiving antimicrobial prophylaxis. Therefore, antimicrobial prophylaxis for Pneumocystis carinii 
pneumonia should be administered for 1 year following transplantation. Cytomegalovirus (CMV) 
prophylaxis is recommended for 3 months after transplantation, particularly for patients at increased risk 
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Skin Cancer Events. Patients on immunosuppressive therapy are at increased risk for skin cancer. 
Exposure to sunlight and ultraviolet (UV) light should be limited by wearing protective clothing and 
using a sunscreen with a high protection factor. 
8.6.5 
Pharmacology – Handling, Storage, Dispensing and 
Disposal 
Mean ± SD Steady State Sirolimus Pharmakokinetic parameters in low- to moderate-immunologic 
risk adult renal transplant patients following 2 mg daily dosing 
 
Whole blood trough sirolimus concentrations, as measured by LC/MS/MS in renal transplant patients, 
were significantly correlated with AUCτ,ss. Upon repeated, twice-daily administration without an initial 
loading dose in a multiple-dose study, the average trough concentration of sirolimus increases 
approximately 2- to 3-fold over the initial 6 days of therapy, at which time steady-state is reached. A 
loading dose of 3 times the maintenance dose will provide near steadystate concentrations within 1 day in 
most patients. 
To minimize variability in sirolimus concentrations, sirolimus should be taken consistently with or 
without food. In healthy subjects, a high-fat meal (861.8 kcal, 54.9% kcal from fat) increased the mean 
total exposure (AUC) of sirolimus by 23 to 35%, compared with fasting. The effect of food on the mean 
sirolimus Cmax was inconsistent depending on the sirolimus dosage form evaluated. 
Management of interacting medications, monitoring of whole blood concentrations and appropriate 
dosage adjustments of immunosuppressant drugs (tacrolimus and sirolimus) will be based on Hematology 
SOPs for GVHD prophylaxis. 
Distribution. The mean (± SD) blood-to-plasma ratio of sirolimus was 36 ± 18 in stable renal allograft 
patients, indicating that sirolimus is extensively partitioned into formed blood elements. The mean 
volume of distribution (Vss/F) of sirolimus is 12 ± 8 L/kg. Sirolimus is extensively bound (approximately 
92%) to human plasma proteins, mainly serum albumin (97%), α1-acid glycoprotein, and lipoproteins. 
Metabolism. Sirolimus is a substrate for both CYP3A4 and P-gp. Sirolimus is extensively metabolized in 
the intestinal wall and liver and undergoes counter-transport from enterocytes of the small intestine into 
the gut lumen. Inhibitors of CYP3A4 and P-gp increase sirolimus concentrations. Inducers of CYP3A4 
and P-gp decrease sirolimus concentrations . Sirolimus is extensively metabolized by O-demethylation 
and/or hydroxylation. Seven (7) major metabolites, including hydroxy, demethyl, and hydroxydemethyl, 
are identifiable in whole blood. Some of these metabolites are also detectable in plasma, fecal, and urine 
samples. Sirolimus is the major component in human whole blood and contributes to more than 90% of 
the immunosuppressive activity. 
Excretion. After a single dose of [14C] sirolimus oral solution in healthy volunteers, the majority (91%) 
of radioactivity was recovered from the feces, and only a minor amount (2.2%) was excreted in urine. The 
mean ± SD terminal eliminatioCorrelative/Special Studies 

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9.0 Correlative/Special Studies 
9.1 Pharmacokinetics 
 
9.1.1 
Clinical Pharmacology Objectives 
Optional Pharmacokinetics samples are being collected to compare the plasma pharmacokinetics of 
clofarabine in patients with varying degrees of renal impairment.  Optional research samples will be 
collected from those patients that provide consent to optional research samples. PK samples will be 
collected for a total of 12 patients with varying degrees of renal impairment, 6 patients from each 
arm: Arm 3- Clofarabine 40mg/m^2 and Melphalan 100mg/m^2 and Arm 4- Clofarabine 30mg/m^2 
and Melphalan 100mg/m^2. If a participant’s sample is not considered “evaluable” another 
participant may be consented until 12 evaluable patients have been completed. 
9.1.2 
Blood Sample Collection 
Blood samples will be collected from an indwelling venous catheter or by venipuncture. The 
PK collection should be done at a separate anatomic site as drug infusion e.g., in the 
opposite arm of the drug infusion or from catheter when drug is infused peripherally. PK 
blood draws are allowed to be drawn from the same central line if the patient has a central 
line where there is more than one lumen port. The PK draws should not be drawn from the 
same lumen port to where the study agent is being administered. 
At each time point indicated in the table below, peripheral blood will be collected into a 
single 7 ml green-top tube (sodium or lithium heparin) containing deoxycoformycin to 
prevent blood clotting and ex vivo deamination of clofarabine. Tubes will be inverted 
several times and then immediately placed on ice for transportation to the CICSL, the 
processing laboratory.  
Blood samples will be collected at the following times during the first cycle: 
 Table 9.2.1  
Time Points of Blood Sample Collection for PK/PD Studies 
Time Point 
Sample Type 
Day 
Hour:minute (h:m) of       
collection (24-hour 
clock) 
Pretreatment(immediately 
prior to Clofarabine 
infusion) *Document 
start time of infusion 
Peripheral blood 
-8 
 
End of clofarabine 
infusion  (within  15 min) 
*Document end time of 
infusion 
Peripheral blood 
-8 
 
2 ± 0.5 hr (after 
completion of the 
infusion) 
Peripheral blood 
-8 
 
4 ± 0.5 hr (after 
completion of the 
infusion) 
Peripheral blood 
-8 
 
Pretreatment: 
(immediately prior to 
Clofarabine infusion) 
Peripheral blood 
-7 
 

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*Document start time of 
infusion 
 
 
 
 
Pretreatment: 
(immediately prior to 
Clofarabine infusion) 
*Document start time of 
infusion 
Peripheral blood 
-5 
 
End of clofarabine 
infusion  (within  15 min) 
*Document end time of 
infusion 
Peripheral blood 
-5 
 
2 ± 0.5 hr (after 
completion of the 
infusion) 
Peripheral blood 
-5 
 
4 ± 0.5 hr (after 
completion of the 
infusion) 
Peripheral blood 
-5 
 
24 hrs from Start Time of 
Day -5  Clofarabine Dose 
Peripheral blood 
-4 
 
 
9.1.3 Sample Processing 
Anti-coagulated whole blood samples (one 10 ml green-top tube that contains 
deoxycoformycin specific for correlative research sample testing) will be processed by 
centrifugation for 10 minutes at 1500 x g at 4⁰ C. The resulting plasma will be transferred to 
appropriately labeled polypropylene tubes and frozen at < -70⁰ C until analysis. 
 
9.1.5   Pharmacokinetic Analytic Method 
For analysis of clofarabine in human plasma, a sensitive and selective LC/MS/MS method 
will be developed and validated in the Analytical Pharmacology Core Facility at the City of 
Hope. 
 
9.1.6   Pharmacokinetic Data Analysis Methods 
Plasma clofarabine PK data will be analyzed using non-compartmental methods to derive the 
following secondary parameters; Cmax, Ctrough, AUC0-24hr, and CLsys). The individual non-
compartmental PK parameters will be summarized for each renal function cohort and 
compared using standard statistical methods.  
 
 
 

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10.0 Study Calendar 
10.1 Pre-transplant study calendar (Conditioning Phase) 
Procedure 
Pre-Study 
screening 
Day -9 
Day -8 
Day -7 
Day -6 
Day -5 
Day -4 
Day -3 
Day -2 
Day -1 
Informed Consent 
x 
 
 
 
 
 
 
 
 
 
Demographic information 
x 
 
 
 
 
 
 
 
 
 
History and Physical 
x 
x 
 
 
 
 
 
 
 
 
Vital signs 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
Height/Weight**** 
x 
x 
 
 
 
 
 
 
 
 
KPS 
x 
x 
 
 
 
 
 
 
 
 
CBC with differential AND ANC 
x 
x 
 
x 
 
x 
x 
x 
x 
x 
PT/PTT 
x 
 
 
 
 
 
 
 
 
 
CMP and Mg 
x 
x 
x 
x 
x 
x 
x 
x 
x 
x 
LDH 
x 
x 
 
x 
 
x 
x 
x 
x 
x 
Ferritin 
x 
 
 
 
 
 
 
 
 
 
Phos, Uric Acid 
x 
x 
 
x 
 
x 
x 
x 
x 
x 
24 hour urine creatinine clearance 
x 
 
 
 
 
 
 
 
 
 
Urine analysis 
x 
 
 
 
 
 
 
 
 
 
Pregnancy test for female patients* 
x 
x 
 
 
 
 
 
 
 
 
Pulmonary function tests 
x 
 
 
 
 
 
 
 
 
 
Echocardiogram/MUGA scan 
x 
 
 
 
 
 
 
 
 
 
Stress test (if applicable) 
x 
 
 
 
 
 
 
 
 
 
EKG 
x 
 
 
 
 
 
 
 
 
 
CT chest 
x 
 
 
 
 
 
 
 
 
 
Chest X-ray** 
 
 
 
 
 
 
 
 
 
 
HSV 1 Antibody 
x 
 
 
 
 
 
 
 
 
 
Hepatitis B Panel (Hepatitis B surface antigen, 
core antibody and surface antibody) 
 
x 
 
 
 
 
 
 
 
 
 
Hepatitis C total antibody; if positive, 
Hepatitis C RNA quantitation 
x 
 
 
 
 
 
 
 
 
 
Syphilis testing by RPR 
x 
 
 
 
 
 
 
 
 
 
HIV-1 antigen or HIV NAT testing, HIV 1 and 2 
antibody 
x 
 
 
 
 
 
 
 
 
 
CMV igG antibody 
x 
 
 
 
 
 
 
 
 
 
ABO/Rh type and antibody screen 
x 
 
 
 
 
 
 
 
 
 

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Immunoglobulin G levels *** 
x 
 
 
 
 
 
 
 
 
 
Lumbar puncture WITH MTX if indicated 
x 
 
 
 
 
 
 
 
 
 
Bone Marrow Biopsy and Aspiration 
x 
 
 
 
 
 
 
 
 
 
Cytogenetics 
x 
 
 
 
 
 
 
 
 
 
TREATMENT 
 
 
 
 
 
 
 
 
 
 
Hydrocortisone (pre-clofarabine) 
 
x 
x 
x 
x 
x 
 
 
 
 
Clofarabine 
 
x 
x 
x 
x 
x 
 
 
 
 
Dexamethasone (pre-melphalan) 
 
 
 
 
 
 
x 
 
 
 
Melphalan 
 
 
 
 
 
 
x 
 
 
 
Tacrolimus 
 
 
 
 
 
 
 
x 
x 
x 
Sirolimus 
 
 
 
 
 
 
 
x 
x 
x 
Toxicity Monitoring 
 
x 
x 
x 
x 
x 
x 
x 
x 
x 
*with childbearing potential; **CXR done weekly during transplant hospitalization; ***Immunoglobulin level checked as per SOP; ****Height 
is not required after the screening visit 
 
10.2 Post-transplant Study Calendar (Stem Cell Infusion and Follow-up) 
Procedure 
Day 0 
Day 30  
± 7 days 
 
Day 100 
± 14 days 
Day 180 
± 28 days 
 
***1 year 
± 28 days 
 
2 years 
± 45 days 
 
3 years 
± 45 days 
 
4 years 
± 45 days 
 
5 years 
± 45 days 
 
History and Physical 
 
x 
x 
x 
x 
x 
x 
x 
x 
Vital signs 
x 
x 
x 
x 
x 
x 
x 
x 
x 
Height/Weight** 
 
x 
x 
x 
x 
x 
x 
x 
x 
KPS 
 
x 
x 
x 
x 
x 
x 
x 
x 
CBC with differential AND ANC 
x 
x 
x 
x 
x 
x 
x 
x 
x 
CMP and Mg 
x 
x 
x 
x 
x 
x 
 
 
 
LDH 
x 
x 
x 
x 
x 
x 
 
 
 
Pulmonary function tests 
 
 
 
 
x 
x 
 
 
 
Echocardiogram/MUGA scan 
 
 
 
 
x 
x 
 
 
 
EKG 
 
 
 
 
x 
x 
 
 
 
Immunoglobulin levels* 
 
x 
x 
 
x 
x 
 
 
 
Bone Marrow Biopsy and Aspiration 
 
x 
x 
x 
x 
x 
 
 
 
Cytogenetics 
 
x 
x 
x 
x 
x 
 
 
 
Chimerism study 
 
x 
x 
x 
x 
x 
 
 
 
TREATMENT 
 
 
 
 
 
 
 
 
 
Stem Cell Infusion 
x 
 
 
 
 
 
 
 
 
Tacrolimus 
          X -------------------------------------------------------------------------† 

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Sirolimus 
          X -------------------------------------------------------------------------† 
Acute/Chronic GVHD Assessment ‡ 
 
x 
x 
x 
x 
x 
x 
x 
x 
CMV qPCR 
 
x 
x 
x 
 
 
 
 
 
Toxicity Monitoring 
x 
x 
x 
 
 
 
 
 
 
*Immunoglobulin level will be checked as per SOP; †Tacrolimus and sirolimus will be tapered as per COH SOP based on donor match and 
presence of GVHD;  ‡GVHD assessment will be done weekly during admission and at indicated clinic visits post-transplant; **Height is not 
required after the screening visit; ***May be done as per treating physician discretion. 
 
 
 
 
 
 
 
 
 

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Procedure 
Day 0 
Day 30  
± 7 days 
 
Day 100 
± 14 days 
Day 180 
± 28 days 
 
***1 year 
± 28 days 
 
2 years 
± 45 days 
 
3 years 
± 45 days 
 
4 years 
± 45 days 
 
5 years 
± 45 days 
 
History and Physical 
 
x 
x 
x 
x 
x 
x 
x 
x 
Vital signs 
x 
x 
x 
x 
x 
x 
x 
x 
x 
Height/Weight*** 
 
x 
x 
x 
x 
x 
x 
x 
x 
KPS 
 
x 
x 
x 
x 
x 
x 
x 
x 
CBC with differential AND ANC 
x 
x 
x 
x 
x 
x 
x 
x 
x 
CMP and Mg 
x 
x 
x 
x 
x 
x 
 
 
 
LDH 
x 
x 
x 
x 
x 
x 
 
 
 
Pulmonary function tests 
 
 
 
 
x 
x 
 
 
 
Echocardiogram/MUGA scan 
 
 
 
 
x 
x 
 
 
 
EKG 
 
 
 
 
x 
x 
 
 
 
Immunoglobulin levels** 
 
x 
x 
 
x 
x 
 
 
 
Bone Marrow Biopsy and Aspiration 
 
x 
x 
x 
x 
x 
 
 
 
Cytogenetics 
 
x 
x 
x 
x 
x 
 
 
 
Chimerism study 
 
x 
x 
x 
x 
x 
 
 
 
TREATMENT 
 
 
 
 
 
 
 
 
 
Stem Cell Infusion 
x 
 
 
 
 
 
 
 
 
Tacrolimus 
          X -------------------------------------------------------------------------† 
Sirolimus 
          X -------------------------------------------------------------------------† 
Acute/Chronic GVHD Assessment ‡ 
 
x 
x 
x 
x 
x 
x 
x 
x 
CMV qPCR 
 
x 
x 
x 
 
 
 
 
 
Toxicity Monitoring 
x 
x 
x 
 
 
 
 
 
 
*CXR done weekly during transplant hospitalization; **Immunoglobulin level will be checked as per SOP; †Tacrolimus and sirolimus will be 
tapered as per COH SOP based on donor match and presence of GVHD; ‡GVHD assessment will be done weekly during admission and at 
indicated clinic visits post-transplant; ***Height is not required after screening; **** May be done as per treating physician discretion. 
 
 
 
 
 
 
 
 
 
 

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11.0 Data Reporting/Protocol Deviations 
11.1 Data Reporting 
11.1.1 Confidentiality and Storage of Records 
Electronic data capture forms will be stored in encrypted, password protected, secure computers/servers 
that meet all HIPAA requirements.  When results of this study are reported in medical journals or at 
meetings, identification of those taking part will not be disclosed.  Medical records of subjects will be 
securely maintained in the strictest confidence, according to current legal requirements.  They will be 
made available for review, as required by the FDA, HHS, or other authorized users such as the NCI, 
under the guidelines established by the Federal Privacy Act and rules for the protection of human 
subjects. 
11.1.2 Subject Consent Form 
At the time of registration, the original signed and dated Informed Consent form, HIPAA research 
authorization form, and the California Experimental Subject’s Bill of Rights (for the medical record) and 
three copies (for the subject, the research record, and the Coordinating Center) must be available.  All 
Institutional, NCI, Federal, and State of California requirements will be fulfilled. 
11.1.3 Data Collection Forms and Submission Schedule  
All data will be collected within 1-2 weeks using standard Medidata Electronic Data Capture (EDC) case 
report forms. Data will be collected and stored on secured computers as indicated in Section 11.1.1.   
11.1.3.1 Eligibility Checklist 
The Eligibility Checklist must be completed by a protocol nurse or clinical research associate and 
electronically signed by an authorized investigator prior to registering the subject.  See Section 4.3 for the 
registration procedure. 
11.1.3.2 Prior Therapy Forms and On-Study Forms 
Within 1-2 weeks of registration, the clinical research associate will submit case report forms. 
11.2 Protocol Deviations 
11.2.1 Deviation Policy 
This protocol will be conducted in accordance with COH’s “Clinical Research Protocol Deviation Policy” 
located at http://www.coh.org/dsmc/Documents/Institutional%20Deviation%20Policy.pdf. 
Deviations from the written protocol that could increase patient risk or alter protocol integrity require 
prior IRB approval of a single subject exception (SSE) request.  In addition, if contractually obligated, the 
sponsor must also approve the deviation.  IRB pre-approved SSE protocol modifications are considered 
an amendment to the protocol and not a deviation.  The submission of a deviation report is not required. 
Brief interruptions and delays may occasionally be required due to travel delays, airport closure, 
inclement weather, family responsibilities, security alerts, government holidays, etc.  This can also extend 
to complications of disease or unrelated medical illnesses not related to disease progression.  The PI has 
the discretion to deviate from the protocol when necessary so long as such deviation does not threaten 
patient safety or protocol scientific integrity.  Examples include, but are not limited to:  a) dose 
adjustments based on excessive patient weight; b) alteration in treatment schedule due to non-availability 
of the research participant for treatment; c) laboratory test results which are slightly outside the protocol 
requirements but at levels that do not affect participant safety.  These instances are considered to be 
deviations from the protocol.  A deviation report will be submitted to the DSMC/IRB within five days. 

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11.2.2 Reporting of Deviations 
All deviations will be reported to the COH DSMC within five days.  The DSMC will forward to report to 
the IRB following review. 
11.2.3 Resolving Disputes 
The COH Investigational Drug Service (IDS) cannot release a research agent that would cause a protocol 
deviation without approval by the PI.  Whenever the protocol is ambiguous on a key point, the IDS 
should rely on the PI to clarify the issue. 
In situations where there is misperception or dispute regarding a protocol deviation among the persons 
involved in implementing the protocol, it is the responsibility of the PI to resolve the dispute and the PI 
may consult with the DSMC chair (or designee) to arrive at resolution. 
 
12.0 Endpoint Evaluation Criteria/Measurement of Effect 
12.1 Primary Endpoints 
12.1.1 Safety Lead-in Segment 
Toxicity is the primary endpoint for the patient safety lead-in segment of this study. Toxicity will be 
scored on both the Bearman Scale and NCI CTCAE v4.03 Scale. We expect Bearman Gr I/II tox in all 
categories and grade 3, 4 CTCAE hematological tox since it is myeloablative conditioning. All grades of 
Bearman toxicities are described in the Appendix B, and the CTCAE v4.3 is available on the internet at 
http://evs.nci.nih.gov/ftp1/CTCAE/CTCAE_4.03_2010-06-14_QuickReference_8.5x11.pdf. 
Unacceptable toxicity in a given patient is defined as any regimen-related grade III/IV toxicity per 
Bearman Criteria, or for hematologic toxicities, per NCI CTCAE v4.03 toxicity criteria, any grade 4 
neutropenia associated with fever or infection and lasting beyond 3 weeks, or grade 4 neutropenia lasting 
for more than 28 days, or any other regimen-related cause of death.  
This unacceptable toxicity definition was established after reviewing two sources of toxicity data (see 
protocol section 2.1): 1) preliminary data from patients conditioned with clofarabine/melphalan (Forman, 
2013 unpublished) and 2) historical data from patients conditioned with fludarabine/melphalan (Forman, 
2013 unpublished; Nakamura 2012). Generally, regimen-related grade I/II toxicity per Bearman Criteria 
occurred in >50% of patients, in at least one toxicity class; this was also true for hematologic toxicity. 
Note: The NCI CTCAE v4.0 scale will also be used for reporting of adverse events and more detailed 
reporting. 
12.1.2 Overall Trial 
The primary endpoint for the trial is 2-year progression-free survival (PFS). Patients are considered a 
failure for this endpoint if they die (regardless of cause) or experience disease progression/relapse. 
Progression-free survival is estimated from the start of treatment to the date of death, disease 
relapse/progression, or last follow-up whichever occurs first.  
12.2 Secondary Endpoints 
12.2.1 Overall Survival (OS) 
Patients are considered a failure for this endpoint if they die, regardless of cause. The time to this event is 
the time from start of treatment until death, or last follow-up, whichever comes first. 
12.2.2 Relapse/Progression (CIR) 
The event is relapse/progression. The time to this event is measured from start of treatment. Deaths 
without relapse/progression are considered a competing risk. Surviving patients with no history of 
relapse/progression are censored at time of last follow-up. 

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12.2.3 Non-Relapse Mortality (NRM) 
Non-relapse mortality (NRM) is defined as death occurring in a patient from causes other than relapse or 
progression. NRM is measured from start of treatment until non-disease related death, or last follow-up, 
whichever comes first. Deaths from relapse/progression are considered a competing risk. 
12.2.4 Toxicities and Adverse Events 
Safety Lead-In Segment and Phase II Study: The worst grade of all toxicities will be collected from day -
9 to day -1, and again from day 0 to 30 post-transplant. Toxicity will be assessed and reported using the 
Bearman [34] and CTCAE v4.03 scales [35]. Safety Lead-In Segment: From day 31 to 100, all post-
transplant toxicities that are considered serious adverse events will be collected. Phase II Study: From day 
31 to day 100 post-transplant, only toxicities that are considered serious adverse events that are at least 
possibly related to the study drug (clofarabine/melphalan) will be collected.  
12.2.5 Acute Graft versus Host Disease (aGVHD) of grades 2-4 
and 3-4 
Acute graft versus host disease is graded according to the Consensus Grading [36] and grading and 
staging tables are included in Appendix C. The first day of acute GVHD onset at a certain grade will be 
used to calculate cumulative incidence curves for that GVHD grade. The endpoint will be evaluated from 
day 0 through 100 days post transplant. 
12.2.6 Chronic Graft versus Host Disease (cGVHD) 
Chronic graft versus host disease is scored according to NIH Consensus Staging [37] as shown in 
Appendix D. The first day of chronic GVHD onset will be used to calculate cumulative incidence curves. 
12.2.7 Infection 
Microbiologically documented infections will be reported by site of disease, date of onset, severity and 
resolution, if any. This data will be captured via case report form and will be collected from day -9 to day 
100 post-transplant and will follow the same data collection intervals as the toxicity and adverse event 
data. 
12.3 Disease Status Assessment  
12.3.1 Complete Remission 
Remission is defined as <5% blasts with no morphological characteristics of acute leukemia (e.g. Auer 
rods) or myelodysplasia in a bone marrow with >20% cellularity, peripheral blood counts showing ANC 
>1000/µL (including patients in CR with incomplete platelet recovery). In addition, normalization of 
cytogenetics must be demonstrated by the absence of previous cytogenetic abnormality identified prior to 
transplantation in the bone marrow aspirate without appearance of new abnormalities.  
12.3.2 Relapse 
Any of the following indicates relapse: 
 
The reappearance of blast cells in the peripheral blood 
 
>5% blasts in the marrow, not attributable to another cause (e.g., bone marrow regeneration) 
 
The appearance of new dysplastic changes within the bone marrow 
 
Development of extramedullary leukemia or leukemic cells in the cerebral spinal fluid 
 
Reappearance of cytogenetic abnormalities present prior to transplantation 

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12.3.3 Disease Persistence /Progression: 
Patient does not achieve CR upon repeat bone marrow examination after therapy and displays persistent 
evidence of disease by cytogenetics in blood or bone marrow consistent with pre-transplant features, or 
consistent with progression of MDS to AML. 
12.4 Study Termination 
All patients will be followed for survival until death or 5 years post transplant, whichever occurs first. For 
patients who relapse/progress, the date of relapse/progression will be recorded, but these patients will no 
longer follow the study calendar for required disease monitoring, however patients will continue to be 
followed for survival. 
All reasons for discontinuation of treatment must be documented. 
Patients may withdraw from the study at any time for any reason. 
 
13.0 Statistical Considerations 
13.1 Study Design  
This study is a single-center, single-arm phase II trial to evaluate the anti-leukemic activity and safety of 
clofarabine (40 mg/m2), given in combination with high-dose melphalan (140 mg/m2), in patients with 
acute myeloid leukemia/acute lymphoid leukemia in remission or myelodysplastic syndrome. The first six 
patients treated on this study will be part of a patient safety lead-in.  
 
Given that the primary endpoint for this trial is 2-year progression-free survival, we recognize that a 
randomized design would be the design of choice where patients would be randomized to receive either 
fludarabine/melphalan or clofarabine/melphalan or one of two doses of clofarabine. We believe that the 
results achieved at COH with the clofarabine/melphalan regimen combination (Figure 4) suggest that the 
results from a single arm trial will be scientifically compelling. This regimen would fit in the category of 
agents that “provide evidence of extraordinary and unanticipated activity compared to prior agents in the 
same class” a category of agents which Cannistra indicates is publishable as a single arm trial with a 
stable historical control [38]).  
 
13.2 Patient Safety Lead-in Segment 
The patient safety lead-in segment of this study will be conducted to ensure there are no unexpected 
toxicities; ultimately we plan to treat 6 patients at what is deemed to be a safe dose level. At the initial 
dose ‘level’ up to 3 patients will be treated with 40mg/m2 of clofarabine and 140 mg/m2 of melphalan.  
Note: no more than 3 patients can be <30 days post stem cell infusion at any time during the patient safety 
lead-in phase. If ≤ 1/6 patients experience an unacceptable toxicity event, the trial will enroll up to an 
additional 59 patients. If, however, > 1/6 patients experience unacceptable toxicity, the dose of melphalan 
will be reduced to 100 mg/m2, with subsequent patients be treated at 40mg/m2 (clofarabine)/100 mg/m2 
(melphalan) dose ‘level’.  
While not expected, if >1/6 patients at the 40mg/m2 (clofarabine)/100 mg/m2 (melphalan) dose level 
experience unacceptable toxicity, the clofarabine dose will be reduced to 30mg/m2 with subsequent 
patients treated at 30mg/m2 (clofarabine)/100 mg/m2 (melphalan) dose ‘level’. Additional dose levels 
below the 30/100 dose level will not be considered. Ultimately a total of 65 patients will be treated at the 
clofarabine/melphalan dose level considered safe as determined during the patient safety lead-in segment 
of this study. With two dose reductions permissible, the overall maximum study sample size could reach 
77. 

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Toxicities will be scored using both the Bearman Scale and the NCI CTCAE v4.0 Scale. To be evaluable 
for toxicity, a patient must start treatment and be observed for 30 days from stem cell infusion or have 
experienced an unacceptable toxicity. All patients who are not evaluable for toxicity will be replaced. 
Unacceptable toxicity in a given patient is defined as any regimen-related grade III/IV toxicity per 
Bearman Criteria, or for hematologic toxicities, per NCI CTCAE v4.0 toxicity criteria, any grade 4 
neutropenia associated with fever or infection and lasting beyond 3 weeks, or grade 4 neutropenia lasting 
for more than 28 days, or any other regimen-related cause of death. Note: The NCI CTCAE v4.0 scale 
will also be used for reporting of adverse events and more detailed reporting. 
13.3 Stopping Rules for Excessive Toxicity 
The following table will be consulted as relevant toxicities are encountered following the patient safety 
lead-in. The early stopping rule for safety/toxicity will be assessed for each patient at day +30 post 
transplant/stem cell infusion. The expected rate of unacceptable toxicity should not be ≥33%. See the 
table below for detailed early stopping rules. Patients with ongoing toxicity (beyond day +30) will be 
followed until resolution or stability.  If more than the specified number of patients has significant 
treatment related toxicities, patient accrual will be halted and a full review of the data by the Data Safety 
Monitoring Committee will be mandated. Patient accrual will not resume until approved by the Data 
Safety Monitoring Committee to do so. 
# of patients 
treated at 
phase II dose 
# of patients with 
unacceptable 
toxicity to halt 
enrollment1 
Cumulative probability of early 
stopping given a toxicity rate of: 
15% 
33% 
45% 
  6 
  2 
0.22 
0.64 
0.84 
12 
  4 
0.24 
0.73 
0.92 
18 
  6 
0.25 
0.78 
0.95 
24 
  8 
0.25 
0.81 
0.97 
30 
10 
0.25 
0.83 
0.98 
36 
12 
0.25 
0.84 
0.99 
42 
14 
0.25 
0.85 
0.99 
48 
16 
0.25 
0.86 
0.99 
54 
18 
0.25 
0.87 
0.99 
60 
20 
0.25 
0.88 
0.99 
1: For each unacceptable toxicity, halt enrollment and evaluate if 
the cumulative # of patients reaches or exceeds the specified limits. 
 
13.4 Stopping Rules for Activity 
After 20 patients have the opportunity to achieve one year of follow-up, the observed PFS rate will be 
compared to our hypothesized alternative rate of 77% using a single sample Log-Rank test. If the 
alternative is rejected at the 0.02 level, patient accrual will be halted and a full review of the data by the 
Data Safety Monitoring Committee will be mandated. Patient accrual will not resume until approved by 
the Data Safety Monitoring Committee to do so. This test is similar is spirit to that of test of futility in the 
SWOG two stage design [39]. Note: The actual discouraging rate will be determined by the proportion of 
AML, ALL and MDS patients accrued and the encouraging rate will be taken as 15% higher. 

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13.5 Sample Size 
Historical Estimates, Fludarabine/Melphalan RIC alloHCT: 
As noted in the Background section, because the available historical data are not reflective of our 
observed RIC fludarabine-melphalan experience (COH PFS estimates are better), 2-year PFS estimates 
were also generated using data from the COH transplant repository from patients transplanted from 2005 
to 2009 using patient selection criteria that match the protocol inclusion criteria. The estimates from these 
analyses are as follows: AML 2-year PFS 60%, ALL 2-year PFS 51% (Forman, 2013 unpublished). 
Using these data, the published MDS outcomes (Nakamura et al. [22]) and expected accrual pattern 
across disease subgroups, the 2-year PFS estimate for fludarabine/melphalan is 62% (95%CI: 57.7-66.5). 
Preliminary Estimate, Clofarabine/Melphalan RIC alloHCT: 
From a similar patient population treated at City of Hope (Khaled 2013, pending publication of ASBMT 
Oral Abstract), the estimated two-year PFS probability for patients conditioned with clofarabine (30/40 
mg/m2) and high dose melphalan (100/140 mg/m2) as part of alloHCT, was reported to be 77.7% (95% 
CI: 57.7 – 89.1). Based on these preliminary estimates, a total of 65 patients are required to detect a 15% 
increase in two-year PFS from the historical COH fludarabine/melphalan estimate of 62% to 77%, with 
approximately 86% power and a 1-sided α=0.05, using the SWOG, single arm non-parametric approach 
(based on work done by Brookmeyer and Crowley [40]).   
Smaller trials (patient subgroups) like the one proposed here are more sensitive to patient variation. The 
sample size calculation used to estimate number of patients and expected difference between historical 
fludarabine-based/RIC patients and clofarabine/melphalan may be impacted if the patients (AML, ALL 
and MDS) are not sufficiently homogeneous. The patient population eligible for this trial will be standard 
alloHCT-eligible patients (except that patients up to age 75 will be allowed) in CR1 or CR2 only. This is 
a healthier population than those treated so far in the phase I study. For this reason, we expect outcomes 
to be comparable to, or somewhat better than those seen in the patients treated with this regimen thus far 
at City of Hope.  
Accrual Estimates:  
Annually City of Hope treats 13 MDS, 26 AML (1CR/2CR), and 5 ALL (1CR/2CR) patients with RIC 
alloHCT using a fludarabine/melphalan preparative regimen. Based on these numbers, if half of these 
patients enrolled, this study expects to accrue roughly 23 patients per year, just under 2 per month. The 
study is expected to complete the enrollment phase of the study in 5 years, with an additional 5 years of 
follow-up required from the time the last patient is enrolled to complete the analysis. 
Statistical Analysis Plan: 
Survival estimates will be calculated using the Kaplan-Meier method. The cumulative incidence of 
relapse/progression and non-relapse mortality will be calculated as competing risks using the Gray 
method. Toxicity information recorded will include the type, severity, and the probable association with 
the study regimen. Tables will be constructed to summarize the observed incidence by severity and type 
of toxicity. Baseline information (e.g. the extent of prior therapy) and demographic information will be 
presented, to describe the patients treated in this study.  
14.0 Human Subject Issues 
14.1 Institutional Review Board 
In accordance with City of Hope policies, an Institutional Review Board (IRB) that complies with the 
federal regulations at 45 CFR 46 and 21 CFR 50, 56 and State of California Health and Safety code, Title 
17,  must review and approve this protocol and the informed consent form prior to initiation of the study.  
All institutional, NCI, Federal, and State of California regulations must be fulfilled. 

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14.2 Recruitment of Subjects 
Patients will be recruited from among candidates for reduced intensity HCT at City of Hope Cancer 
Center for acute leukemia or MDS.  Individuals will be recruited from the COH campus and from the San 
Gabriel Valley and environs (~25 mile radius) using the City of Hope Website and a quarterly e-
newsletter sent to local hematologists/oncologists listing our ongoing clinical trials. 
14.3 Advertisements  
No advertisements will be used to recruit potential study subjects.  
14.4  Study location and Performance Sites 
This study will be performed at COH.   
14.5 Confidentiality  
This research will be conducted in compliance with federal and state of California requirements relating 
to protected health information (PHI).  The study will record toxicity, disease response, survival and 
toxicity data, and this will be linked to the subject’s identity using a coded study number.  In addition, 
results of screening tests to rule out HIV, HBC, and HCV performed in the Department of Transfusion 
Medicine will be used with the participant’s permission if performed in the past 4 months.  The principal 
investigator, co-investigators, and laboratory technicians will have access to this information, but all 
information will be treated confidentially.  No identifiers will be used in any subsequent publication of 
these results.   
14.6 Financial Obligations and Compensation 
The investigational drug clofarabine, will be provided free of charge by Sanofi-Aventis.  Should this drug 
become commercially available during the course of treatment, the research participant and/or the insurance 
carrier may be asked to pay for the costs of the clofarabine. 
The standard of care drug(s) and procedures provided will be the responsibility of the research participant 
and/or the insurance carrier.  The research participant will be responsible for all copayments, deductibles, 
and other costs of treatment and diagnostic procedures as set forth by the insurance carrier.  The research 
participant and/or the insurance carrier will be billed for the costs of treatment and diagnostic procedures 
in the same way as if the research participant were not in a research study.  However, neither the research 
participant nor the insurance carrier will be responsible for the research procedures related to this study. 
In the event of physical injury to a research participant, resulting from research procedures, appropriate 
medical treatment will be available at the City of Hope to the injured research participant, however, 
financial compensation will not be available. 
The research participant will not be paid for taking part in this study. 
14.7 Informed Consent Processes  
The Principal Investigator or IRB approved named designate will explain the nature, duration, purpose of 
the study, potential risks, alternatives and potential benefits, and all other information contained in the 
informed consent document.  In addition, they will review the experimental subject’s bill of rights and the 
HIPAA research authorization form.  Research subjects will be informed that they may withdraw from the 
study at any time and for any reason without prejudice, including as applicable, their current or future 
care or employment at City of Hope or any relationship they have with City of Hope.  Research subjects 
will be afforded sufficient time to consider whether or not to participate in the research. 
Before signing the study consent form, HIPAA authorization form and the Experimental Subject’s Bill of 
Rights, research subjects will undergo an assessment of their comprehension of the study by the Research 
Subject Advocate.  Should sufficient doubt be raised regarding the adequacy of comprehension, further 
clarifications will be made and the questionnaire repeated until a satisfactory result is obtained.  

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Prospective research subjects who cannot adequately comprehend the fundamental aspects of the research 
study with a reasonable amount of discussion, education and proctoring will be ineligible for enrollment.  
For those subjects who do comprehend the fundamental aspects of the study, consent will be obtained and 
documented, followed by eligibility testing.  The research team will review the results of eligibility 
testing and determine if the subject is a candidate for study enrollment.  

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15.0 References 
1. 
Bonate PL, Arthaud L, Cantrell WR, Jr., Stephenson K, Secrist JA, 3rd, Weitman S. Discovery 
and development of clofarabine: a nucleoside analogue for treating cancer. Nat Rev Drug Discov 
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2. 
Bensinger WI, Martin PJ, Storer B, et al. Transplantation of bone marrow as compared with 
peripheral-blood cells from HLA-identical relatives in patients with hematologic cancers. N Engl J Med 
2001;344:175-181. 
3. 
Michallet M, Thomas X, Vernant JP, et al. Long-term outcome after allogeneic hematopoietic 
stem cell transplantation for advanced stage acute myeloblastic leukemia: a retrospective study of 379 
patients reported to the Societe Francaise de Greffe de Moelle (SFGM). Bone Marrow Transplant 
2000;26:1157-1163. 
4. 
Suciu S, Mandelli F, de Witte T, et al. Allogeneic compared with autologous stem cell 
transplantation in the treatment of patients younger than 46 years with acute myeloid leukemia (AML) in 
first complete remission (CR1): an intention-to-treat analysis of the EORTC/GIMEMAAML-10 trial. 
Blood 2003;102:1232-1240. 
5. 
Weiden PL, Flournoy N, Thomas ED, et al. Antileukemic effect of graft-versus-host disease in 
human recipients of allogeneic-marrow grafts. N Engl J Med 1979;300:1068-1073. 
6. 
Sullivan KM, Weiden PL, Storb R, et al. Influence of acute and chronic graft-versus-host disease 
on relapse and survival after bone marrow transplantation from HLA-identical siblings as treatment of 
acute and chronic leukemia. Blood 1989;73:1720-1728. 
7. 
Slavin S, Nagler A, Naparstek E, et al. Nonmyeloablative stem cell transplantation and cell 
therapy as an alternative to conventional bone marrow transplantation with lethal cytoreduction for the 
treatment of malignant and nonmalignant hematologic diseases. Blood 1998;91:756-763. 
8. 
Alyea EP, Kim HT, Ho V, et al. Comparative outcome of nonmyeloablative and myeloablative 
allogeneic hematopoietic cell transplantation for patients older than 50 years of age. Blood 
2005;105:1810-1814. 
9. 
Sayer HG, Kroger M, Beyer J, et al. Reduced intensity conditioning for allogeneic hematopoietic 
stem cell transplantation in patients with acute myeloid leukemia: disease status by marrow blasts is the 
strongest prognostic factor. Bone Marrow Transplant 2003;31:1089-1095. 
10. 
Bertz H, Potthoff K, Finke J. Allogeneic stem-cell transplantation from related and unrelated 
donors in older patients with myeloid leukemia. J Clin Oncol 2003;21:1480-1484. 
11. 
Deeg HJ, Shulman HM, Anderson JE, et al. Allogeneic and syngeneic marrow transplantation for 
myelodysplastic syndrome in patients 55 to 66 years of age. Blood 2000;95:1188-1194. 
12. 
King KM, Damaraju VL, Vickers MF, et al. A comparison of the transportability, and its role in 
cytotoxicity, of clofarabine, cladribine, and fludarabine by recombinant human nucleoside transporters 
produced in three model expression systems. Mol Pharmacol 2006;69:346-353. 

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13. 
Xie C, Plunkett W. Metabolism and actions of 2-chloro-9-(2-deoxy-2-fluoro-beta-D- 
arabinofuranosyl)-adenine in human lymphoblastoid cells. Cancer Res 1995;55:2847-2852. 
14. 
Xie KC, Plunkett W. Deoxynucleotide pool depletion and sustained inhibition of ribonucleotide 
reductase and DNA synthesis after treatment of human lymphoblastoid cells with 2-chloro-9-(2-deoxy-2-
fluoro-beta-D-arabinofuranosyl) adenine. Cancer Res 1996;56:3030-3037. 
15. 
Genini D, Adachi S, Chao Q, et al. Deoxyadenosine analogs induce programmed cell death in 
chronic lymphocytic leukemia cells by damaging the DNA and by directly affecting the mitochondria. 
Blood 2000;96:3537-3543. 
16. 
Kirschbaum MH, Stein AS, Popplewell L, et al. A Phase I Study in Adults of Clofarabine 
Combined with High-Dose Melphalan as Reduced-Intensity Conditioning for Allogeneic Transplantation. 
Biol Blood Marrow Transplant 2012;18:432-440. 
17. 
van Besien K, Stock W, Rich E, et al. Phase I-II Study of Clofarabine-Melphalan-Alemtuzumab 
Conditioning for Allogeneic Hematopoietic Cell Transplantation. Biol Blood Marrow Transplant 
2012;18:913-921. 
18. 
Farag SS, Wood LL, Schwartz JE, et al. Phase I trial and pharmacokinetic study of high-dose 
clofarabine and busulfan and allogeneic stem cell transplantation in adults with high-risk and refractory 
acute leukemia. Leukemia 2011;25:599-605. 
19. 
Mineishi S, Magenau J, Tobai H, et al. Allogeneic Hematopoietic Stem Cell Transplantation with 
Clofarabine/Busulfan x 4 (CloBu4) Conditioning Exhibits Significant Anti-Tumor Activity In Non - 
Remission Hematologic Malignancies, Especially In AML. ASH Annual Meeting Abstracts 2010;116:35-. 
20. 
McClune BL, Weisdorf DJ, Pedersen TL, et al. Effect of Age on Outcome of Reduced-Intensity 
Hematopoietic Cell Transplantation for Older Patients With Acute Myeloid Leukemia in First Complete 
Remission or With Myelodysplastic Syndrome. J Clin Oncol 2010;28:1878-1887. 
21. 
Marks DI, Wang T, Perez WS, et al. The outcome of full-intensity and reduced-intensity 
conditioning matched sibling or unrelated donor transplantation in adults with Philadelphia chromosome-
negative acute lymphoblastic leukemia in first and second complete remission. Blood 2010;116:366-374. 
22. 
Nakamura R, Palmer JM, O'Donnell MR, et al. Reduced intensity allogeneic hematopoietic stem 
cell transplantation for MDS using tacrolimus/sirolimus-based GVHD prophylaxis. Leuk Res 
2012;36:1152-1156. 
23. 
Waud WR, Schmid SM, Montgomery JA, Secrist JA, 3rd. Preclinical antitumor activity of 2-
chloro-9-(2-deoxy-2-fluoro-beta-D- arabinofuranosyl)adenine (Cl-F-ara-A). Nucleosides Nucleotides 
Nucleic Acids 2000;19:447-460. 
24. 
Yamauchi T, Nowak BJ, Keating MJ, Plunkett W. DNA repair initiated in chronic lymphocytic 
leukemia lymphocytes by 4-hydroperoxycyclophosphamide is inhibited by fludarabine and clofarabine. 
Clin Cancer Res 2001;7:3580-3589. 
25. 
Stephenson K, Wilson S, Schmid SM, Waud WR, Craig A, Weitman S. Correlation between 
frequency of administration and efficacy of clofarabine in the H460 human non-small cell lung tumor 
xenograft model. Annual Meeting of the American Association for Cancer Research (AACR). 
Washington, D.C.; 2003:A814. 

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26. 
Zhenchuk A, Lotfi K, Juliusson G, Albertioni F. Mechanisms of anti-cancer action and 
pharmacology of clofarabine. Biochem Pharmacol 2009;78:1351-1359. 
27. 
Bonate PL, Arthaud L, Stuhler J, Yerino P, Press RJ, Rose JQ. The distribution, metabolism, and 
elimination of clofarabine in rats. Drug Metab Dispos 2005;33:739-748. 
28. 
Kantarjian HM, Gandhi V, Kozuch P, et al. Phase I Clinical and Pharmacology Study of 
Clofarabine in Patients With Solid and Hematologic Cancers. J Clin Oncol 2003;21:1167-1173. 
29. 
Kantarjian H, Gandhi V, Cortes J, et al. Phase 2 clinical and pharmacologic study of clofarabine 
in patients with refractory or relapsed acute leukemia. Blood 2003;102:2379-2386. 
30. 
Faderl S, Gandhi V, O'Brien S, et al. Results of a phase 1-2 study of clofarabine in combination 
with cytarabine (ara-C) in relapsed and refractory acute leukemias. Blood 2005;105:940-947. 
31. 
Jeha S, Gandhi V, Chan KW, et al. Clofarabine, a novel nucleoside analog, is active in pediatric 
patients with advanced leukemia. Blood 2004;103:784-789. 
32. 
Jeha S, Gaynon PS, Razzouk BI, et al. Phase II study of clofarabine in pediatric patients with 
refractory or relapsed acute lymphoblastic leukemia. J Clin Oncol 2006;24:1917-1923. 
33. 
Karp JE, Ricklis RM, Balakrishnan K, et al. A phase 1 clinical-laboratory study of clofarabine 
followed by cyclophosphamide for adults with refractory acute leukemias. Blood 2007;110:1762-1769. 
34. 
Bearman SI, Appelbaum FR, Buckner CD, et al. Regimen-related toxicity in patients undergoing 
bone marrow transplantation. J Clin Oncol 1988;6:1562-1568. 
35. 
Cancer Therapy Evaluation Program, National Cancer Institute, National Institues of Health. 
Common Terminology Criteria for Adverse Events (CTCAE) Version 4.03. 2010. 
36. 
Przepiorka D, Weisdorf D, Martin P, et al. 1994 Consensus Conference on Acute GVHD 
Grading. Bone Marrow Transplant 1995;15:825-828. 
37. 
Filipovich AH, Weisdorf D, Pavletic S, et al. National Institutes of Health consensus 
development project on criteria for clinical trials in chronic graft-versus-host disease: I. Diagnosis and 
staging working group report. Biol Blood Marrow Transplant 2005;11:945-956. 
38. 
Cannistra SA. Phase II trials in journal of clinical oncology. J Clin Oncol 2009;27:3073-3076. 
39. 
Green SJ, Dahlberg S. Planned versus attained design in phase II clinical trials. Stat Med 
1992;11:853-862. 
40. 
Brookmeyer R, Crowley J. A confidence interval for the median survival time. Biometrics 
1982;38:29-41. 
 

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Appendix A: Karnofsky Performance Status Scale 
 
Karnofsky 
Scale % 
Karnofsky Description 
100 
Normal, no complaints, no evidence of disease. 
90 
Able to carry on normal activity, minor symptoms 
or signs of disease. 
80 
Normal activity with effort, some signs or 
symptoms of disease. 
70 
Cares for self, unable to carry on normal activity or 
to do active work. 
60 
Requires occasional assistance, but is able to care 
for most of own needs. 
50 
Requires considerable assistance and frequent 
medical care. 
40 
Disabled, requires special care and assistance. 
30 
Severely disabled, hospitalization is indicated 
although death is not imminent. 
20 
Hospitalization necessary, very sick, active 
supportive treatment necessary. 
10 
Moribund, fatal processes 
Dead 
 
 

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Appendix B: Modified Bearman Scale [34] 
 
Grade I 
Grade II 
Grade III 
Cardiac 
toxicity 
Mild EKG abnormality, not 
requiring medical intervention; or 
noted heart enlargement on chest 
x-ray with no clinical symptoms 
Moderate EKG abnormalities requiring 
and responding to medical 
intervention; or requiring continuous 
monitoring without treatment; or 
congestiveheart failure responsive to 
digitalis or diuretics  
Severe EKG abnormalities with 
no or only partial response to 
medical intervention; or heart 
failure with no or only minor 
response to medical 
intervention; or decrease in 
voltage by more than 50%  
Bladder 
toxicity 
Macroscopic hematuria after 2 
days from last chemotherapy 
dose with no subjective 
symptoms of cystitis and not 
caused by infection  
Macroscopic hematuria after 7 days 
from last chemotherapy dose not 
caused by infection; or hematuria after 
2 days with subjective symptoms of 
cystitis not caused by infection  
Hemorrhagic cystitis with frank 
blood, necessitating invasive 
local intervention with 
installation of sclerosing 
agents, nephrostomy or other 
surgical procedure  
Renal 
toxicity 
Increase in creatinine up to twice 
the baseline value (usually the 
last recorded before start of 
conditioning)  
Increase in creatinine above twice 
baseline but not requiring dialysis  
Requirement of dialysis  
Pulmonary 
toxicity 
Dyspnea without chest x-ray 
changes not caused by infection 
or congestive heart failure; or 
chest x-ray showing isolated 
infiltrate or mild interstitial 
changes without symptoms not 
caused by infection or congestive 
heart failure  
Chest x-ray with extensive localized 
infiltrate or moderate interstitial 
changes combined with dyspnea and 
not caused by infection or CHF; or 
decrease of PO2 (> 10% from 
baseline) but not requiring mechanical 
ventilation or > 50% O2 on mask and 
not caused by infection or CHF 
Interstitial changes requiring 
mechanical ventilatory support 
or > 50% oxygen on mask and 
not caused by infection or CHF  
Hepatic 
toxicity 
Mild hepatic dysfunction with 
bilirubin ≥ 2.0 mg/dL and ≤ 6.0 
mg/dL or weight gain > 2.5% and 
< 5% from baseline, of non-
cardiac origin; or SGOT increase 
more than 2-fold but less than 5-
fold from lowest preconditioning  
Moderate hepatic dysfunction with 
bilirubin > 6.0 mg/dL and < 20 mg/dL; 
or SGOT increase > 5-fold from 
preconditioning; or clinical ascitis or 
image documented ascitis > 100 mL; 
or weight gain > 5% from baseline of 
non-cardiac origin  
Severe hepatic dysfunction 
with bilirubin > 20 mg/dL; or 
hepatic encephalopathy; or 
ascitis compromising 
respiratory function  
CNS 
toxicity 
Somnolence but the patient is 
easily arousable and oriented 
after arousal  
Somnolence with confusion after 
arousal; or other new objective CNS 
symptoms with no loss of 
consciousness not more easily 
explained by other medication, 
bleeding or CNS infection  
Seizures or coma not explained 
(documented) by other 
medication, CNS infection, or 
bleeding  
Stomatitis 
Pain and/or ulceration not 
requiring a continuous IV 
narcotic drug  
Pain and/or ulceration requiring a 
continuous IV narcotic drug (morphine 
drip)  
Severe ulceration and/or 
mucositis requiring preventive 
intubation; or resulting in 
documented aspiration 
pneumonia with or without 
intubation  
GI toxicity 
Watery stools > 500 mL but < 
2,000 mL every day not related to 
infection  
Watery stools > 2,000 mL every day 
not related to infection; or macroscopic 
hemorrhagic stools with no effect on 
cardiovascular status not caused by 
infection; or subileus not related to 
infection 
Ileus requiring nasogastric 
suction and/or surgery and not 
related to infection; or 
hemorrhagic enterocolitis 
affecting cardiovascular status 
and requiring transfusion  

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Note: Grade IV regimen-related toxicity is defined as fatal toxicity 
Appendix C: Acute GVHD Grading and Staging [36] 
Extent of Organ Involvement  
Stage  
Skin  
Liver  
Gut  
1  
Rash on <25% of skina  
Bilirubin 2-3 mg/dlb  
Diarrhea > 500 ml/dayc or 
persistent nausead  
2  
Rash on 25-50% of skin  
Bilirubin 3-6 mg/dl  
Diarrhea >1000 ml/day  
3  
Rash on >50% of skin  
Bilirubin 6-15 mg/dl  
Diarrhea >1500 ml/day  
4  
Generalized erythroderma 
with bullous formation  
Bilirubin >15 mg/dl  
Severe abdominal pain 
with or without ileus  
 
Gradee  
I  
Stage 1-2  
None  
None  
II  
Stage 3 or  
Stage 1 or  
Stage 1  
III  
—  
Stage 2-3 or  
Stage 2-4  
IVf  
Stage 4  
Stage 4  
—  
 
a. Use “Rule of Nines” (Table 4) or burn chart to determine extent of rash.  
b. Range given as total bilirubin. Downgrade one stage if an additional cause of elevated bilirubin has 
been documented.  
c. Volume of diarrhea applies to adults. For pediatric patients, the volume of diarrhea should be based on 
body surface area. Downgrade one stage if an additional cause of diarrhea has been documented.  
d. Persistent nausea with histological evidence of GVHD in the stomach or duodenum.  
e. Criteria for grading given as minimum degree of organ involvement required to confer that grade.  
f. Grade IV may also include lesser organ involvement with an extreme decrease in performance status. 

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Appendix D: Chronic GVHD Scoring [37]